Previously classified US documents suggest that the Indonesian President, Susilo Bambang Yudhoyono, was implicated in a cover-up of an ambush in Papua in 2002.
Three people, including two US citizens, died in the incident which clouded relations with the US.
The documents released through a Freedom of Information Act Request show that Mr Yudhoyono, as then coordinating minister of political and security affairs, tried to stall FBI attempts to probe the matter.
He reportedly acted when a police investigation implicated the miliitary in the fatal shooting.
An academic at the University of California, Dr Eben Kirksey, says Mr Yudhoyono brought politics into a case which should have been about forensic facts.
A Papuan man, Antonius Wamang, was jailed for life for the shooting, with researchers saying he was linked to the military.
Susilo Bambang Yudhoyono is seeking re-election as Indonesia's president next week.