The only Indonesian jailed over the violence surrounding East Timor's 1999 vote for independence has launched a legal challenge against the court that convicted him.

Former militia leader Eurico Guterres has asked Indonesia's Constitutional Court to review the legality of the Indonesia Human Rights Tribunal which found him guilty of the violence.

Guterres, who was born in East Timor, is currently serving 10 years in a Jakarta prison for failing to control his militia group which attacked a pro-independence shelter, massacring 11 men and a child.

His lawyer Mahendradatta said the formation of the ad hoc court had been politically driven. "Eurico Guterres felt discriminated by a political decision (at that time)," he said. "With the establishment of the Human Rights Tribunal, (he) felt his constitutional right was deprived."

The Human Rights Appeal Tribunal halved the 10 years sentence in 2004, but it was later reinstated by Supreme Court.

In his petition to the court, Guterres has called on the Constitutional Court to dismiss the Human Rights Court. His lawyer said if the bid succeeds, he should be freed from all charges.

Guterres in March testified before the controversial East Timor-Indonesia Commission of Truth and Friendship, which is seeking a "conclusive truth" about the 1999 bloodshed in order to aid reconciliation between the two countries. He denied killing anyone, but added that if his men had killed anyone, he had been held responsible with his 10 year sentence.

Other than Guterres, the Tribunal tried 17 defendants, including Indonesian generals, military and police officers working in East Timor in 1999, but acquitted them either at the lower or the appeal stage.

Indonesia's military has been accused of forming militia groups, including Guterres' Aitarak (Thorn) group in the lead up to the 1999 ballot. The militia groups, backed by the Indonesian forces, have been blamed for 1,500 deaths across the tiny half-island in the months surrounding the historic vote.