Indonesia is hoping a new security treaty with Australia will uphold the sovereignty of both countries, including restive areas such as Papua, Indonesia's Foreign Minister Hassan Wirajuda says.

The treaty, due to be signed on Monday, was almost scuppered after Australia granted visas this year to 43 Papuan asylum seekers who claimed they were being persecuted.

Wirajuda told reporters the pact did not specifically say that Australia rejected Papuan independence, but that the issue was implicit in its wording.

"There is a provision in which Australia and Indonesia will not support any separatist movement directed against one side," he said. "Certainly, its main principle will be applicable when we talk about separatism in Papua. A treaty has a long time span and it will bind any kind of government in Australia as well as in Indonesia."

Indonesia tore up a defence pact with its southern neighbour seven years ago after the Australian-led intervention in East Timor. Both countries have spent two years negotiating this latest treaty, which also includes cooperation in anti-terrorism and nuclear issues.

The pact has been slammed by some Australian opposition politicians and non-governmental groups, who argue it could give a free hand to suppress groups seeking independence in Papua.

Australian Greens leader Bob Brown described the pact as "undemocratic and repugnant".

John Dowd, the president of the International Commission of Jurists, said the treaty would allow for increased military cooperation at a time when Indonesian forces were being used against some people in Papua. "The treaty should also include provisions for human rights monitors and foreign journalists to be allowed access," Dowd said in a statement.

Foreign Minister Alexander Downer said the new pact did not mean Australia will reject more Papuan asylum seekers, or that pro-Papuan independence groups in Australia would be banned.