Leaked military documents show Indonesia is engaged in a vast illegal surveillance operation against ordinary people in the restive eastern region of Papua, Human Rights Watch said Monday.

The documents, obtained by Australia's Fairfax newspapers, reveal the "deep military paranoia" that exists in Jakarta toward any kind of free political expression by Papua's indigenous Melanesian majority, the watchdog said.

Hundreds of pages of documents dated 2006 to 2011 include logs of military surveillance of civilians and reports on peaceful political activities.

Many of the reports were prepared by the Kopassus special forces unit. The United States last year resumed links, including limited joint training, with Kopassus, citing improvements in its human rights record.

"The Kopassus documents show the deep military paranoia in Papua that conflates peaceful political expression with criminal activity," Human Rights Watch deputy Asia director Elaine Pearson said in a statement.

"Its outrageous in a modern democratic country like Indonesia that activists, clergy, students and politicians are the targets of military surveillance," she said.

"By treating news conferences, demonstrations and meetings like clandestine criminal activities, the military shows its disregard for fundamental rights in Papua.

"The military should immediately end its harassment and surveillance of civil society."

The documents reveal the military's belief that anyone who tries to expose human rights abuses in Papua, where some activists say Indonesia is guilty of genocide against the indigenous people, is supporting separatism, Pearson said.

Under Indonesian law, peaceful political acts such as displaying the Morning Star flag of Papuan independence are punishable by lengthy prison terms.

Indonesia denies allegations of widespread human rights violations by the armed forces in Papua, but it refuses to allow foreign journalists and rights workers to visit the area to conduct independent inquiries.

"The military conveniently claims that documenting human rights violations in Papua is a front for separatism," Pearson said.

"Such a mind-set endangers the life of every activist in Papua."

Human Rights Watch demanded that Indonesia's government "order the military to cease the unlawful monitoring immediately, and to ensure that civilian authorities retain responsibility for basic law enforcement".

The documents published over the weekend in The Sydney Morning Herald and The Age newspapers also include lists of foreigners such as lawmakers, academics, reporters and religious leaders who allegedly support Papuan separatism.

They include 40 members of the US Congress, South Africa's Archbishop Desmond Tutu, former Papua New Guinea prime minister Sir Michael Somare, and an Australian current affairs show host.

Indonesian officials were unavailable to comment on the documents.

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