Brendan Nicholson – A new security treaty with Jakarta will include an assurance that Australia respects Indonesia's integrity – including its ownership of West Papua – says Prime Minister John Howard.

Indonesia has insisted on the inclusion of an assurance that Australia will not seek independence for the troubled province as a condition to be met, before it signs the security agreement.

Mr Howard said he expected to meet Indonesia's President Yudhoyono soon, though the exact date was still to be worked out.

"Some time in the not too distant future we will meet and talk about a lot of things," Mr Howard said.

"Our relationship with Indonesia is very important. I am perfectly happy in any document that we sign to say that we respect the territorial integrity of Indonesia."

Mr Howard said Australia's relationship with Indonesia was always challenging because the two countries were very different, but he said he had a good personal relationship with President Yudhoyono.

"There's a lot of trust at senior government levels and there's always been a lot of trust maintained at other levels. I hope that we will have a very productive meeting when we do get together, which will probably be later this month."

Mr Howard said the security pact would be one of a number of issues covered. "I noticed something in the newspapers about that this morning based on comments made by the President's security adviser. It is an issue that we need to kick around," Mr Howard said.

"There is no argument about our attitude towards Indonesian sovereignty over Papua. We've never had a view that Papua should separate from Indonesia. The changes that have been made in Papua by the Indonesian Government have provided a lot more democracy, a lot more freedom," he said. "People should bear that in mind when they automatically criticise Indonesia every time something goes wrong."