Foreign aid organisations plan to suspend operations in Aceh province because of advice from the Indonesian Government about "security concerns".
Michael Elmquist, the head of the United Nations Office for the Co-ordination of Humanitarian Affairs in Jakarta, told BBC News Online that the agencies were "left with little choice" but to follow the advice.
"In the longer term, we hope to revert to normal procedures," he said.
Foreign ministry spokesman Marty Natalegawa said that all humanitarian assistance would now be distributed by local government officials and the Indonesian Red Cross.
But the move will add to international concerns about the humanitarian situation in Aceh, as the Indonesian military's crackdown against separatist rebels from the Free Aceh Movement (Gam) entered its ninth day.
Binny Buchori, Executive Secretary of the International NGO Forum on Indonesian Development, told the BBC's East Asia Today programme that there was still a clear need for humanitarian assistance in Aceh.
"I would question why the UN would support and agree with the Indonesian government's request," she said.
"The Indonesian government does not have the capacity to help the Acehnese people on their own... and I think in this case the UN is just trying to be diplomatic."
There were also signs the unrest is spilling over into the Indonesian capital, after a group of youths attacked the Jakarta offices of Kontras, a prominent Indonesian human group.
The mob, who said they were from Pemuda Panca Marga, an organisation with links to the Indonesian military, smashed furniture and accusing Kontras of being pro-Gam.
In Aceh, the Indonesian military said 76 separatist rebels have now been killed - a figure Gam disputes.
The military reported further clashes with Gam rebels and said it had seized Pulo Nasi island, off the coast from the provincial capital Banda Aceh.
The army said the island had been used as a Gam training camp.
The army also released a report on Tuesday which denied it had killed civilians in the coastal town of Cot Rabu last week.
The report acknowledged that 10 people had been shot dead in the town, but insisted that all 10 were rebels, not civilians, according to the Associated Press.
Aid suspension
The government's advice to foreign aid workers has been issued because of security concerns, according to the Indonesian foreign ministry.
"We know that Gam wants to attract international attention by, among other things, disturbing foreigners," spokesman Marty Natalegawa told the French agency AFP.
He said that some foreign aid agencies had operated in Aceh without proper co-ordination with the authorities, making it difficult for the government to protect them.
The World Bank also announced on Tuesday that it had suspended a $7.5 m a year aid programme in Aceh at the request of the Indonesian Government.
The programme provided aid to some 1.7m people, the bank's co-ordinator in Aceh, Thomas Walton, told the German press agency DPA.
According to the Asia Wall Street Journal, the bank cited increasing security risks and a military clampdown on public gatherings as reasons for the pullout.
International concern
Since the military offensive began last Monday, there has been growing international concern about the humanitarian situation in Aceh.
On Monday, Amnesty International condemned the reported killings of civilians, including children.
It laid the blame on both the government and the rebels, urging both sides to make the protection of civilians a priority.
International agencies are also concerned that adequate supplies of aid continue to get through to the Acehnese people.
Food prices have risen sharply in recent days due to attacks on lorries plying the main supply routes in and out of the province.
The International Red Cross told the BBC that more supplies were urgently needed - adding that volunteers have had to handle days-old corpses without protective clothing.
The government acknowledged that its response to the humanitarian crisis had been slow, but on Monday Indonesian troops started guarding supply trucks bringing in food and other essentials from the neighbouring province of Medan.
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