A 2004 report by a group of students at Yale Law School, entitled Indonesian Human Rights Abuses in West Papua: Application of the Law of Genocide to the History of Indonesian Control, found strong evidence of genocide against indigenous Papuans. The Centre for Peace and Conflict Studies at the University of Sydney published a report in 2005 called "Genocide in West Papua?" which says that without action the very survival of the indigenous people of Papua is seriously threatened.

However, both reports have been criticised by the Belgium-based think tank International Crisis Group, in a paper called "Papua: Answers to Frequently Asked Questions", which says that the Yale report has many factual errors and neither paper makes a strong case that genocide has occurred. The ICG says that reporting on Papua is often distorted and tries to give evidence-based answers to many contentious questions.

ICG has published several other reports on Papua, which can be found on its Indonesia page.

Amnesty International offers an authoritative collection of documents on human rights abuses in Papua.

The Internal Displacement Monitoring Centre (IDMC) has a collection of useful articles about the territory.

The president of the Fellowship of West Papuan Baptist Churches launched a report in March 2007 describing recent violent episodes and giving a critique of Special Autonomy.

The circumstances surrounding the 2001 death of separatist leader Theys Eluay were described in The Economist. You have to subscribe if you want to download the whole article.

The Washington East-West Center has done a number of useful reports, including a 2004 study of Jakarta's attitudes to Papua

If you find yourself musing on the Papuans' original grievance about the Act of Free Choice that wed them to Indonesia, you might like to read a 2005 study by P.J. Drooglever, commissioned by the Dutch government.

The West Papua Report is a regular update from the West Papua Advocacy Team (WPAT) and East Timor and Indonesia Action Network (ETAN). Previously it was produced by the Robert F. Kennedy Centre for Human Rights.

A good source of English-language news items on Papua is Kabar Irian News, although it hasn’t been updated for a while.

Campaigning sites on Papua abound, and include the site of the Free Papua Movement. Its old site remains open, with useful information. The new site is known as Solidarity South Pacific. Also worth trying are the site of the West Papuan Institute for Human Rights Study and Advocacy (Elsham) in Jayapura and the Indonesia Human Rights Campaign, Tapol.

Some of the best sites for the latest updates on Papua are the West Papua Independence Movement and Peace Movement Aeotearoa, a New Zealand non-governmental organisation which collects news from a variety of sources dating back to 1999.

Indonesia has its own National Commission on Human Rights, Komnas HAM. The Indonesian Legal Aid Foundation (YLBHI), a leading human rights organisation in the country, has papers on civil, political and human rights issues in Indonesia

The New York Times did a thorough investigation in late 2005 into the activities of Freeport McMoRan at its vast mine in Timika. Smaller articles on the same topic include one by Greenleft.org.

Australia's difficult relationship with Indonesia over the issue of Papua was analysed in an essay in April 2006 by Richard Chauvel of Victoria University in Melbourne. And a report published by the West Papua Project in March 2007, entitled Blundering In?, looks at the new security treaty between Australia and Indonesia and the effect it might have on Papua.