Australia and Indonesia have signed an historic new security treaty, but critics say the treaty raises concerns over Australia's ability to fulfil its human rights obligations in the region.

Foreign Minister Alexander Downer and his Indonesian counterpart, Hassan Wirajuda, signed the document on the Indonesian island of Lombok on November 13.

The treaty covers 10 main areas, including defence, law enforcement, counter-terrorism, intelligence and maritime security, but human rights concerns hinge specifically on article two, which prohibits either country from supporting activities that may threaten each other's territorial integrity or sovereignty.

While the treaty acknowledges Australia's domestic laws that respect international obligations to provide asylum to genuine refugees, critics say the agreement is a deliberate attempt to prevent Australia from responding to human rights violations in West Papua.

The president of the International Commission of Jurists (ICJ) in Australia, John Dowd, says his organisation has serious concerns about Indonesia's handling of its jurisdiction over West Papua and the treaty should be the subject of more public debate.

"I can see no basis for a treaty with a country that's not under attack and we're not under attack," he told the ABC. "I think it's a mask for assisting their military."

The ICJ claims Indonesia has not honoured an international agreement made in 1962 that West Papuans be given the right to self-determination.

The Australian ICJ has released a specific statement on West Papua, which notes that no democratic elections have ever been held in the territory. The statement refers to a litany of human rights violations perpetuated by Indonesian security forces and the military since Indonesia's occupation.

The Greens Leader, Bob Brown, says the treaty is an "obsequious concession to Jakarta", which will prevent Australia from helping to bring democracy to the region.

"The Howard Government says it will actually suppress people who want to work towards independence for West Papua," he told the ABC. "That's undemocratic."

Alexander Downer said the Australian Government had never supported separatist movements, but with obvious reference to East Timor added: "I mean unless we actually decided in the case of a foreign country that we thought that country should be broken up, we would give no comfort or support to separatist movements."

Kevin Rudd, the opposition spokesman for foreign affairs, said Labor believed West Papua to be part of Indonesia, but supported "an effective and real autonomy" for the West Papuan people.