Indonesia declared martial law in Aceh in May
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Indonesia has been accused of widespread abuses in its campaign against separatists in Aceh province.
The New York-based Human Rights Watch (HRW) issued a report based on interviews with refugees who alleged extra-judicial killings, arbitrary arrests and attacks on civilians.
HRW's Saman Zia-Zarifi told the BBC that Jakarta had imposed a "shroud of secrecy" in Aceh.
But Indonesia defended its military, saying troops faced a "war situation."
Mr Zia-Zarifi said Indonesian troops were moving into villages and attacking civilians.
"We heard of numerous instances of people who were killed very brazenly out in the open," he said.
The 50-page HRW report includes accounts of specific cases.
"I saw one of the soldiers handcuff the ankles of this man, and then another soldier held him by his feet and swung him against a tree," one witness is quoted as saying.
"The soldier did this many times so that the man's head was hitting the tree. His brains were coming out of his head, until he was dead," he said.
'War situation'
HRW has said that the Indonesian army is indiscriminately targeting young Acehnese men, many of whom have nothing to do with separatist rebels from the Free Aceh Movement (Gam).
"We got numerous testimonies about people who had been killed... suspected of being members of Gam, or Gam supporters... none of these people were armed or were wearing uniforms," Mr Zia-Zarifi said.
Indonesia's ambassador to London, Juwono Sudarsono, said that atrocities were also carried out by Gam, and that the actions of the Indonesian military had to be seen in the context of a "war situation".
"Once you have soldiers on the ground who are facing terrorist organisations like Gam, there is no way that any commander can have immediate operational control over the troops," he told the BBC's East Asia Today programme.
HRW has said it is aware that Gam is also responsible for attacking civilians, but it said it was unable to assess Gam's activities because, along with other organisations, HRW is not allowed into Aceh.
Mr Sudarsono said Jakarta was keeping groups like Human Rights Watch out of Aceh because they were biased against the Indonesian operation, and he defended some of the violence carried out by troops.
"You cannot have legal accountability in a war situation... no Geneva convention can apply as you see also in Iraq," he said.
Officially, the Indonesian Government has said that 1,200 rebels have been killed since the offensive began in May, but observers say it is impossible to confirm any figures because of the restrictions on international organisations entering the province.
HRW is calling on Jakarta to open up Aceh, but it also wants other countries to take more of an interest.
"The international community seems to have fallen somewhat silent," Mr Zia-Zarifi said.