Karen Michelmore – The Federal Government has given a clear commitment under a new security pact to oppose Indonesian separatist movements, including those operating within Australia, Indonesia has said.

Australia and Indonesia will next week sign the security agreement, which reinforces cooperation on defence, police, intelligence and counter-terrorism. Under the pact, both nations have also promised to respect each others territorial integrity and not support secessionist movements.

It comes as the countries move to repair relations, damaged earlier this year when Australia granted temporary protection to 43 asylum seekers from the separatist Indonesian province of Papua.

"Besides principles of respecting territorial integrity, sovereignty, not interfering in domestic affairs – one important principle in this agreement is that both parties will not use or support separatist movements and will not use their territory as a standing point for separatist movements," Indonesian Foreign Minister Hassan Wirajuda said today.

He said Prime Minister John Howard had guaranteed earlier this year that Australia "would not be used as bases or staging (posts) for separatists". "And now it's in the framework of a security agreement," Mr Wirajuda said. While there was no specific mention of Papua in the agreement, the "principle" of rejecting separatism was applicable.

In a letter to Indonesian President Susilo Bambang Yudhoyono ahead of a meeting in June, Mr Howard said Australia did not support separatism and secessionist movements in Indonesia. He also pledged that no Australian development funding would be used to fund such activities. "My Government does not wish to see Australia become a staging point for any such activities," the letter read.

Today, Mr Wirajuda said it was a clear commitment, but did not say what Indonesia expected Australia to do in order to meet the pledge. "Certainly this framework agreement will be the guiding principle on how Indonesia manages its relations with Australia and vice versa," he said. "It's a question of principle that's very clear, there's no doubt about that. That commitment is no longer verbal, but a treaty-based commitment."

The wide-ranging agreement also includes cooperation in tackling problems of people smuggling, money laundering, terrorism, corruption, illegal fishing, cybercrime and drug trafficking.

However, Mr Wirajuda said it was different to the deal reached in 1995 between the two nations, which Indonesia tore up in 1999 following the crisis in East Timor. "It's not a security pact, compared to Indonesia's security agreement in 1995," Mr Wirajuda said.

"The 1995 agreement was more like a security pact – there the main element was in case one country was facing threats from a third party, then both countries would help each other. In the security agreement that will be signed, there's no such thing." He said Australia and Indonesia's relationship had had "its ups and downs", but the latest agreement was a historic move.

"The framework of security agreement is something... that we hope is an important contribution to improve the relationship between Indonesia and Australia," he said.