The secret documents, leaked to Fairfax Media, target religious leaders, political activists and even Papuan university students who live outside the troubled province.
They highlight the Indonesian government's paranoia about the pro-independence movement in Papua and its sensitivity towards claims of human rights violations.
Indonesian President Joko Widodo, elected in July 2014, promised to take a new approach to Papua.
He has visited Papua several times, released six political prisoners, including Papua's most famous political prisoner Filep Karma, vowed to stop transmigration to Papua and announced the lifting of restrictions on foreign media in Papua.
However the 2016 Human Rights Watch world report says suppression of the rights to freedom of expression and association in Papua continued.
The “Papuan Action Plan”, dated March 2014 - months before Joko came to power - is branded with the logo of the Indonesian State intelligence Agency or BIN and purports to come from the "Deputy-II Chief" of BIN.
The agency said an internal investigation would be “immediately” launched into the source of the documents following questions from Fairfax Media.
“BIN has never issued such a document,” said BIN's director for information, Sundawan Salya. “We are an intelligence operation and therefore would never use such an open document.”
The dossier lists the strengths and weaknesses of numerous Papuans and describes tactics to "suppress the movement" and "divide and fragment" opinion within the movement.
The pro-independence movement in Papua is especially sensitive in Indonesia given its experience with East Timor, which voted to break away from the republic in 1999.
Markus Haluk, the former chairman of the Central Highlands Papuan Student Association, is one of the Papuans named in the documents.
It is reported that he attends seminars demanding a “liberated Papua” and always criticises government policies.
His strengths are his ability to motivate Central Highland people who are not university educated and create “propaganda via media”. His weaknesses? “Money and women”.
“I think it's harassment of my pride, my character,” Haluk told Fairfax Media. “I have a wife, I am not a playboy. I know there are many ways Indonesia (achieves its goals). It's intelligence strategy, Jakarta's strategy to kill a fighter.”
Haluk said he would not be afraid or panic. “My struggle is to save Papuans. I am not sponsored or paid by anyone. And I will keep fighting until the truth is upheld in Papua.”
The documents list a “minima” and “maximal” goal for each Papuan named in the dossier, which authorities hoped to achieve between April and October 2014.
The “minimal” goal tended to be that the person would not contend there were severe human rights violations in Papua or would reject Papuan independence.
The “maximal” goal was usually that the person would support the Republic of Indonesia or support a draft law on enhancing special autonomy in Papua that former president Susilo Bambang Yudhoyono's government was trying to push through at the time.
Haluk said he did not consider the intelligence agency's strategy to have been a success.
“Papua has been incorporated into Indonesia since the late 1960s but people are still hoisting the (banned West Papuan national) Morning Star flag in the forests, protests demanding (that) Papua separates from Indonesia are still going on,” he said.
Beny Dimara, a prominent religious figure who works with Papuan university students in Yogyakarta, is named in the documents as someone who “follows separatist politics”.
However he told Fairfax Media he had nothing to do with pro-independence activities.
“I am a priest and my concern is only one and that is making young Papuans better in their knowledge of God and in their education.”
Indonesia has a history of spying on Papuans. Documents from Indonesia's elite special forces unit Kopassus, leaked to Fairfax Media in 2011, revealed members of the small armed resistance as well as ordinary Papuans were under intense surveillance.
The 2006-2009 intelligence briefs revealed informants infiltrated every aspect of daily life, including American tourists being watched while they attended a traditional dance outside the capital Jayapura in case they met with pro-independence groups.
Agus Sumule, a lecturer from the University of Papua, said Papuans are the only ethnic group in Indonesia spied on by their own government.
“Indonesians approach Papuans with racism and a paternalistic attitude,” Agus said. “The feeling of being part of Indonesia is not there for Papuans because of the stigma put on Papuans that we are separatists, that we are not able to do things as the Javanese people do, for instance.”
A 2015 report by the directors of the Institute for Policy Analysis for Conflict in Jakarta said Papua struggled with some of the lowest development indicators in the country.
“Successive Indonesian administrations have failed to resolve these problems or reduce the grievances that fuel the independence movement,” it said.
This was despite the implementation of limited special autonomy since 2001 and vast amounts of development spending.
Last May dozens of activists from the West Papua National Committee, a pro-independence group, were arrested during peaceful rallies in Jayapura.
And the government has still not released results of official investigations into the shooting of five protesters by security forces in the town of Enarotali in December 2014.
Theologian and activist Benny Giay, who is described in the documents as a “prominent clergyman who can influence and can generate separatist enthusiasm”, said surveillance was a reality in Papua.
“This is paranoid, this is crazy," he said, when told about the documents. “They are often following us or sending journalists to interview us on certain topics. They will attend press conferences, attend our church meetings.”
Dr Giay said Jokowi, as the president is popularly known, had told the world he was addressing Papua but had done little except announce new road construction.
“I told Jokowi it will take generations to build trust because the problem is a lack of trust from Papuans towards the military,” Dr Giay said.