An Indonesian army officer suspected of involvement in last year's murder of a Papuan independence leader said the man had died suddenly while being questioned by soldiers, his lawyer said.

"Lieutenant Colonel Hartomo said that Theys [Hiyo Eluay] died suddenly, maybe because of shock, while his subordinates were questioning him in his car," said lawyer Ruhut Sitompul.

Hartomo, who like many Indonesians has only one name, commanded the Tribuana task force based in the provincial capital Jayapura when Theys was found dead in his car on November 11 last year. The independence leader had been abducted the previous evening.

"Hartomo was not in the car and had not ordered Theys' questioning. It was the initiative of several of his subordinates," Sitompul told AFP.

Hartomo's reported account of the death does not appear to match the medical facts. An autopsy determined Eluay had suffocated and his body was found in his crashed car with his face darkened and tongue protruding.

Army chief General Endriartono Sutarto has said witness testimony indicated the possible hand of members of the army special forces, Kopassus, who make up most of the Tribuana task force.

The provincial police chief, the governor and rights activists have also alleged military involvement.

Theys headed the peaceful pro-independence movement Papua Presidium Council. He was abducted while driving home from a ceremony at the Tribuana headquarters.

Sitompul quoted Hartomo as saying that, according to reports he had received from his subordinates, Theys was being questioned about his pro-independence sentiments.

"Hartomo seems to think that Theys had died of shock while he was being questioned in his car," the lawyer said.

Hartomo has been detained as a suspect and is believed to be one of three officers who will stand trial in a military court for their alleged involvement in the murder.

Six lower-ranking soldiers will also face trial. The nine, who have not been officially identified, face a maximum 15 years in jail if convicted.

A low-level armed struggle for independence in Papua began after the Dutch ceded control of the resource-rich territory to Indonesia in 1963. Eluay's organisation advocated peaceful pressure for separation.

The province, formerly known as Irian Jaya, was renamed Papua this year under an autonomy law and promised a much greater share of revenue from natural resources.