US authorities have charged an Indonesian man with the 2002 murder of two American teachers at a US copper mine in Indonesia's Papua province.
Police and the FBI have been investigating the attack since 2002
The indictment described Anthonius Wamang as a separatist rebel commander.
Indonesia hopes the charges will end speculation that its troops were involved in the attack and prompt the US to restore military assistance.
But a Papuan human rights activist based in New York claimed Mr Wamang in fact has links to Indonesia's military.
Mr Wamang, 32, is charged with two counts of murder, eight counts of attempted murder, seven counts of causing serious bodily harm and two firearms charges.
It is alleged he took part in an ambush on 31 August 2002 on a road close to PT Freeport Indonesia, a unit of US-based Freeport-McMoRan Copper and Gold Inc, one of the world's largest producers of copper and gold.
Three people were shot dead - two American nationals and an Indonesian.
At least 11 other people were injured in the attack. Most of the victims were teachers at the international school set up for Freeport employees.
"The US Government is committed to tracking down and prosecuting terrorists who prey on innocent Americans in Indonesia and around the world," said Attorney General John Ashcroft.
The indictment charges Mr Wamang with being an operational commander with the Free Papua Movement (OPM), which has been waging armed resistance against Jakarta since its incorporation into the Republic of Indonesia in 1963.
But John Rumbiak, a Papuan activist who lives in exile in the US, said his investigations pointed to links between Mr Wamang and the military.
He told BBC News Online that for the last six or seven years Mr Wamang had been working in the sandalwood and gold panning industries, which Indonesia's Kopassus special forces are traditionally involved with, and has been observed to fly regularly between Papua and Jakarta for meetings with military officials.
He also claimed that OPM was unlikely to have carried out the ambush near Freeport because the group only has two guns, and yet police investigations suggest more than 100 rounds were fired.
"That suggests that someone supplied [the attackers] with guns and ammunition, and who has the ammunition, who has the guns, if not the Indonesian military?" he said.
Marty Natalegawa, spokesman for the Indonesian Foreign Ministry, dismissed the allegations by Mr Rumbiak as "absolutely rubbish".
"I think this is not even worth giving credibility [to] by responding," he told BBC News Online.
"It's a clear case of the US Department of Justice, and nothing else than the attorney general himself.... coming to a conclusion, and issuing this indictment."
He said the Freeport ambush had been one of the stumbling blocks in getting the ban on military ties between Indonesia and the US lifted, and that the US Congress should now take the indictment of Mr Wamang into account.
The US Congress has voted to renew a ban on military ties with Indonesia until it is satisfied Jakarta is co-operating with an FBI probe into the attack.
Military links with Indonesia have been restricted since a 1991 massacre in East Timor in which the Indonesian military was accused of being involved.