Jonathan fled to Bali where he told BBC News Online what it was like to be beaten by the militia

As the violence escalates following the East Timor referendum, BBC News Online users put their questions to Jonathan. Read his replies below.

Gil Alves, East Timor: I heard that you were attacked by militias. Would you please tell me about that? I am very sorry for what happened to you. Thanks for all your great contributions to East Timorese peace.

Jonathan Head: I get such a good response from Timorese people when I'm there. Most of the time the media have a wonderful reception in East Timor, especially when we first went there. Now they are getting a bit more used to journalists, there have been a lot of us there recently, but a few months ago when there weren't so many journalists, and especially two or three years ago when I first started going, you got an extraordinary sense from the Timorese that they wanted to tell their stories.

With regard to the militias, we know why they're doing it. They're targeting journalists because they don't want the truth about East Timor to come out. The attack on me was a very quick event. It was one of those things that can happen to any journalist in a fast moving situation. I was with three of my colleagues, we had gone in to investigate gun fire around the UN Headquarters. Obviously that was very serious - violence had been happening in many parts of East Timor but not at the very Headquarters of the UN in Dili.

When we got there, there was a lot of automatic gunfire, that usually means militia or police, they are the ones that have the most automatic weapons. We took shelter behind a small concrete building because of the bullets, and we were waiting to see what would happen, when suddenly militia men dressed in black started running very fast towards us form three different directions. They were coming straight for us, shouting at us, waving weapons, they had clubs and machetes. We just started running, but because they were coming from different directions we got caught by two of them. They pulled a tape recorder from me and were beating us. We managed to get away, but in my attempt to run away I fell over, and I assumed they would use their knives on me, but one of them kicked me and another one tried to club me with his rifle and at that point an Indonesian intelligence officer, an army guy, not Timorese, who was with them, ordered the militias to stop.

That was very interesting for me to see. He asked us to go over to the military post where there were soldiers standing there, and we sat down there and an extraordinary irony, the same man that had chased me with a knife and kicked me to the ground then came over to the military post. He talked to the soldiers for a while, they clearly told him that he shouldn't be trying to kill foreign journalists, and he came over and explained that he had been very emotional and asked if he could escort us to safety. It was almost unreal.

I think what was most striking, and this is very important for the world to know, the Indonesian military are there with the militias. It was quite clear that a lot of the military intelligence officers work with the militias. There was a Timorese man beaten and shot to death literally 30 metres away from me and no more, just five minutes before I was beaten by the same men who attacked me. The military intelligence man did nothing to save him. Clearly he thought he did not want a foreign journalist to be killed in front of the cameras. It is as cynical as that, and this is the tragedy of East Timor.

This is not a civil war between two evenly matched sides. There are people who genuinely do not want East Timor to become independent, but I think a lot of those may reluctantly and with some guarantees accept the results of referendum. But there is an armed minority, many of them criminals in the past who have been working with the Indonesians for a long time, who are being encouraged and organised to sabotage this democratic choice, and I could see this in action as I was attacked.

Richard Mort, Singapore: Jonathan, I (and I'm sure many others) greatly admire what you are doing - especially when your life was put in peril recently. But tell me, how do your family react when they read and hear that you were nearly killed just doing your job? Don't they tell you to come home?

Jonathan Head: They don't tell me to come home because they know I wouldn't do that, they know how much I love this country - East Timor and Indonesia. It's my job. For most journalists, including myself, 99 % of the time it is fairly routine, there really isn't too much risk. We journalists are remarkably lucky, we have been left alone and widely respected, both by the Indonesian authorities and by people who are often embroiled in horrible conflicts of their own.

This time I think, especially with the scenes on television that my family saw, it was worrying. The other problem in East Timor is telecommunications, the phones don't work very well and so it is difficult for me to get on to my family. I didn't realise when I was attacked I was being filmed, I had no idea. It was colleagues of mine from CNN that filmed me. When I realised that the footage would be seen in London the first thing that I did was call my mother and father to warn them.

I was fine, I was lucky but I wasn't seriously hurt, just a little shaken, but obviously when they saw the footage they would be very worried. I think deep down my mother was extremely anxious about it, but I think she has got used to the idea, and she knows I don't take risks every day. Of course if I thought I was going to face something like these armed militia men I would not have chosen to be there, they just came so fast and so suddenly out of nowhere.

Jeremy Hall, UK: Has your recent experience altered your sense of objectivity?

Jonathan Head: I hope not. It wasn't as traumatic as it might have looked from the pictures. I was aware even as I was being hit that this is something many Timorese have endured ten times over for nearly 24 years.

When you know that, and you know what East Timor has been through, and I have been following this story now for half of my life, I know it quite well, one small brush with violence at the hands of the militias can't really affect your judgement of the story.

Having said that, it is very very hard to be totally dispassionate about East Timor. This is a very black and white issue in many ways. Indonesia illegally invaded the territory and inflicted possibly one of the most savage occupations in recent history on the impoverished and isolated people of this territory, and for years the international community completely ignored it, which to some degree has been corrected now.

Jonathan Head began answering your questions from East Timorese capital Dili

If you are a journalist covering that, if you see what the East Timorese have been through, the number of families you meet who have lost incredible numbers of their relatives in the most appalling fashion, who have endured the most unbelievable hardship, you can't really be dispassionate.

You care deeply about East Timor if you are here, most of my colleagues do as well, and you care deeply about a good outcome. I can accept the intellectual arguments that say East Timor logically could be part of Indonesia, that's fine, if they could choose an alternative. The bottom line is they have experienced unbelievable harshness under the Indonesians and most of them would accept almost anything that is different. I know that from talking to them, and from coming here for the past four years as a reporter, and from covering the story and following it for the last 18 years, and I think most of my colleagues would agree with me.

Manuel Leal, Belgium: If, as it seems, the vast majority of the population of Timor supports independence, where do the militias get their support from? If their only support is the Indonesian army, do you believe that the militias will disappear if and when the former goes away?

Jonathan Head: I think it basically boils down to the fact that this is a very small country which was very divided and had very little prospects for standing on its own two feet, even when the Portuguese left in 1975. It was invaded by a much larger country, Indonesia, by a very powerful military machine, which is used to running its own population with all sorts of dirty tricks, intelligence games.

Jonathan Head is beaten

Early on in the invasion the Timorese were won over through inherent disunity, divisions between them. They would play one village off against another that had some dispute over land. This was happening from the very beginning of the Indonesian invasion in the mid 1970's, and you have now got a very large body of Timorese who have worked with the Indonesians and who have carried out all sort of horrible deeds for them - going into people's houses, abducting them, killing them.

You have also got a lot of people who work officially with the Indonesian army, who have now gone unofficially into the militias. And you have a large number of people who were brought in from outside East Timor. The man who beat me up the other day admitted he was from a neighbouring island, which has no stake in this country.

All those people, often from criminal elements of society, have worked for the Indonesians, they are terrified of being left behind, and they are also clearly following the orders of the Indonesians at the moment. We have had Indonesian intelligence officials out in the field with them, we have seen that. In a small country like this, perhaps only ten or twenty thousand of them, with the full backing of the Indonesian military, are capable of causing real chaos, that's what they're doing at the moment. It is a tragedy, but it is a legacy of this very brutal and bitter invasion.

Kevin, USA: Are the pro-Indonesian militias aware the high level of international media coverage of the East Timor vote? Aren't they guaranteeing the presence of an international peace keeping force by killing and beating unarmed civilians in front of the media?

Jonathan Head: The sad thing is I don't think they are really aware of what they are doing at all in the international context. Many of them, and I know this from having talked to them, are not very well educated, some can't even read or write. They are basically following orders. They have their own concerns, their own instincts, they may be from particular areas that don't get on very well with other areas. If they have worked for the Indonesians they have reason to fear what will happen to them under independence.

It is very interesting, I find, that they target foreign journalists so much, when they can have no concept of how we are covering the story. We are obviously not giving them very good publicity, they are killing a lot of people. It is a one-sided fight this, I have been here long enough to know that. But none of the people who have attacked me and my colleagues are aware of what the BBC or any of the international media are doing. They are being told simply attack Europeans, Americans, whites, westerners and journalists because they are bad for you, and they have no other concept than that.

It is tragic because they have no real long-term future here. The East Timorese people, we have seen this time and time again, do not like the militias, and they desperately want a peaceful outcome to the problem of East Timor which allows them dignity and a degree of self respect. The militias are simply delaying that in the most bloody and violent fashion possible.

Jonathan Head: It is very hard to read exactly what the intentions of people in Jakarta are, because of course the situation in Jakarta itself is pretty chaotic at the moment as well. You have a transitional government, you have a military which is having to get used to the idea of possibly not having the influence it has had over the whole country for the past 30 years, and is very uneasy about that.

I think President Habibe and many of his key allies are genuinely committed to seeing the East Timor problem resolved, however painful that is for Indonesia and its reputation. I think they accept that it is a small impoverished country that is costing Indonesia very big in terms of its international reputation. I am not saying that they love the Timorese or are doing it out of human kindness, but they recognise that this is a problem which needs a resolution.

The thinking may be very different in military circles and we just don't know how high that goes. The military have run this as their own playground for the past 23 years. For them now to be told by the international community that they have got it wrong and they have got to get out is extremely uncomfortable, and at the very least they appear to be willing to allow mayhem to erupt in East Timor, to let the militias out on the streets to cause bloodshed and violence before they leave, if nothing else perhaps to prove they were needed after all.

Whether they really intend to prevent the move towards independence, which is almost bound to follow the results of this referendum, it is hard to say. I doubt that somehow. I don't think they could possibly imagine that would succeed. But we do find it very difficult to know their intentions. Sadly of course what they are doing at the moment is perpetuating the kind of suffering they have inflicted for the past 23 years on the East Timorese people.

Ian Hylton, Hong Kong: Putting the violence to the side for a moment, just how ready is East Timor for independence? Does it have the infrastructure and economy to be viable as an independent state, or do you foresee it relying on forgone aid for years to come?

Jonathan Head: Not at the moment. I think everyone accepts that. It was a desperately impoverished and isolated territory in 1975 when the Indonesians invaded it. Indonesia has put some infrastructure in, but it is not very good. Most people here do not have good education or good jobs, and I think it will be a very long haul for East Timor to be able to make it some kind of viable self government.

In a way that doesn't really matter because the whole principle here is that countries are entitled to decide their own futures. It was accepted by the Portuguese and by the United Nations in 1975 that the East Timorese should have that and the Indonesians have deprived them of it.

Why does it matter to the rest of the world? Because if there is anything like an international order, a sense of international justice and fair play, East Timor is one of the most flagrant examples of those principles being violated. Unless it is resolved, then there is no international order or international justice. Having had that voice, should they choose independence, the international community owes them at least, given its neglect over the past 24 years, enough help to get them started. Then they may be on their own and they will face the same challenges and difficulties that other countries have. They may not make a good job of it, but they are entitled to have a go.

Will Thomas, UK: What are the implications for other Indonesian regions eager to break free from Jakarta's governmental rule, now that East Timor seems to have succeeded in its struggle for independence? Could civil unrest affect neighbouring states, and what effect on the South East Asian balance of power might this have?

Jonathan Head: In theory it should not be too serious because Indonesia, although it is a very fragmented country, an artificial construction out of the old Dutch Empire, a collection of islands spanning the size of the United States, which is the logic for it being a country, but East Timor was always controlled by the Portuguese. The Indonesians who support giving the East Timorese a say over their future accept that they can draw a line here, accept that this was never a part of the old Dutch empire, and they can let it go and still keep the rest of the archipelago together.

But there are serious grievances in other parts of the archipelago, most noticeably in the most north western province of Aceh and in the former Dutch half of New Guinea, Irian Jaya. Their people have experienced equal harshness under military occupation and there are very strong separatist movements there too. They have been encouraged undoubtedly by the East Timorese experience and by the willingness of the Indonesian governments to make concessions and we have much more active separatists movements there now than we had under the authoritarian Suharto regime.

The Indonesian government insist that they cannot make the same concessions for them, if it does that then it really does face the prospect of break-up as has happened to the former Yugoslavia and the former Soviet Union, and they are sending that message out as best they can. I have heard government spokesmen saying to the Acehenese and the Irian Jayanese please accept you are not the same as East Timor. You cannot break free, we will fight to the death to stop you doing so otherwise our country will be dismembered.

But the government will have to find a better way of dealing with these people. At the moment the only option they understand is the military option which has proved to fail in East Timor and to have failed in those territories too, and whatever new government emerges at the end of this year in Indonesia, it is going to have to have both courage and imagination in trying to persuade all the disparate parts of the Indonesian Archipelago that it is worth being part of this country.

I personally hope that it succeeds. So much is wonderful about Indonesia, it could be a great country. But so much is wrong with the way it has been run in the past 30 years that a lot of corrections have got to be made, and an awful lot of grievances and abuses have to be addressed. There has to be a process of people actually seeing justice being done, of abuses being acknowledged by the government, and a long period of healing before this country can live together as one large archepelagic nation.

James Morris, South Africa: How do the East Timorese feel about the West, which has allowed 200,000 of them to be murdered?

Jonathan Head: There is a remarkable amount of faith still among the Timorese people in what the international community can do for them. For most of the past 24 years they have been completely abandoned. I can remember following events in East Timor in the mid 1980's when nobody, and I mean absolutely nobody apart from a few activists, were interested, and the most terrible things were happening then.

The Timorese went through that without anybody raising a voice for them, or very few people, and yet even now younger generations of Timorese, who have known nothing but Indonesian rule, still have an incredible belief that somehow the international community will eventually help them. Obviously they think that is what is happening at the moment.

When the United Nations first got to East Timor about three months ago, the UN found the Timorese just hanging around outside their compound believing that this was finally the liberation they hoped for, and they were going to get a real choice over their future. Sadly that hasn't happened. They are not aware yet how little the UN can do in the current circumstances. It is not a full blown UN mission with peacekeepers. The only reason there is a UN presence at all is because the Indonesian Government which has a total grip on East Timor finally realised that something had to give, it had to make concessions.

I hope in the end that good will come of this, that the Timorese will enjoy the fruits of the choice that they have made in this referendum, but I think there will be a lot of disappointment that the process which seemed to offer so much hope has turned into such a mess at the moment.