A prominent Papuan activist jailed for raising an outlawed separatist flag has been released after Indonesia granted him a pardon, an official said on Thursday.

Yusak Pakage was arrested in 2004 in the Papuan capital of Jayapura for flying the Morning Star flag as part of a ceremony commemorating the 1962 declaration of Papuan independence. He was sentenced in 2005 to ten years in jail for subversion.

"We set him free on Wednesday following a presidential decree dated on June 24 that accepted the pardon request from Yusak Pakage," said Nazarudin Bunasthe, head of the Justice and Human Rights Ministry's Papua office. "He was supposed to be free in 2013," he added.

Bunas said this was the first presidential pardon granted to a political prisoner in Papua.

Benny Giay, a prominent Papuan activist, said the pardon represented slim progress on a myriad problems in Papua. "Despite Pakage's release, the threat for Papuan people to be easily sent to jail remains high," he told AFP.

Indonesian courts have handed stiff penalties, including life in prison, to people caught with separatist symbols such as the Papuan flag.

More than 170 people are in prison for peacefully promoting separatism in Indonesia, most of them from Papua or the eastern Maluku islands, according to Human Rights Watch.

Indonesia took control of Papua, a former Dutch colony on the western half of New Guinea island, in 1969 after a vote among a select group of Papuans widely seen as a sham.

Papuans have long accused Indonesia's military of violating human rights in the province and complain that the bulk of earnings from its rich natural resources flow to Jakarta.

Indonesia also released on Wednesday Papuan political prisoner Chosmos Yual, who was sentenced to six years in jail for his role in a violent pro-independence rally in Jayapura in 2006, Bunas said.