Damning evidence: The use of torture made headlines in 2010 when Fairfax Media published video showing two men being interrogated by Indonesian security forces.

Damning evidence: The use of torture made headlines in 2010 when Fairfax Media published video showing two men being interrogated by Indonesian security forces. Photo: Supplied

Indonesia has been accused of using torture as a ''mode of governance'' in West Papua - security forces have committed at least one incident of torture, on average, every six weeks for the past half century, a study has found.

The research, which collected documentation on 431 cases of torture from 1963 to 2010, found that most West Papuans tortured were ''innocent civilians'' targeted as part of a ''policy of terror''. In only 0.05 per cent of torture cases reviewed were the accused found to be members of the armed resistance. Victims were most commonly farmers and students.

A low-level separatist insurgency has been waged in the former Dutch colony since Indonesia took control of the province in 1963.

Researcher Budi Hernawan, a Catholic brother, said he believed the incidences of torture over the 48-year period were much higher than the 431 cases he drew on.

His findings came to light as three West Papuan activists climbed into the Australian consulate in Bali on Sunday to deliver a letter to Prime Minister Tony Abbott calling for international journalists to be allowed into West Papua and for the release of political prisoners from Indonesian jails. Last week Mr Abbott told journalists he was confident West Papuans could have ''the best possible life … as a part of an indissoluble Indonesia''.

Dr Hernawan, who worked with the Catholic Commission for Justice and Peace in the West Papuan capital of Jayapura for more than a decade, collected the information on torture from the records of local and international human-rights organisations, churches and anthropologists.

Human-rights researchers affirmed the key finding of the study, which was conducted as part of Dr Hernawan's PhD, that ''torture has been deployed strategically by the Indonesian state in Papua as a mode of governance''. The study says Indonesian forces carried out torture as a public spectacle to achieve ''maximum terrifying impact'' on the civilian population in the Papuan provinces, doing so with ''almost complete impunity''.

Torture included beating, kicking, burning, stabbing, shooting, rape, starvation, forced exercise and public humiliation and was carried out by military personnel and to a lesser extent police officers.

In response, the Indonesian embassy in Canberra said: ''Budi's [Hernawan] research at the ANU and the conclusion he arrives at adds to the rich and open discourse of Indonesian history, but any allegation of torture would be met swiftly by the Indonesian people and media themselves, who are ever more critical of any human-rights abuses and the slightest government improprieties.''

Human-rights researcher Abigail Abrash Walton, from the University of Antioch in New England, said torture was a ''systematic strategy for dealing with guerilla warfare'' and had remained the same regardless of changes in Indonesian leadership.

Torture in Papua made international headlines in 2010 when Fairfax Media published a mobile phone video showing two men, Tunaliwor Kiwo and Telangga Gire, being interrogated by Indonesian security forces, one with a knife to his throat and the other screaming as a burning stick was poked at his genitals.

Indonesian President Susilo Bambang Yudhoyono condemned the action and promised a transparent investigation, but the three soldiers each received a sentence of less than a year.

Mr Abbott's office did not respond to a request for comment.