The Australia Secretary for International Development Assistance, Bob McMullan, says his government discusses issues around Papua with Indonesia a lot.
This is despite complaints by the Australia West Papua Association that issues around Indonesia's troubled eastern region are never addressed at the bilateral visits that have become more frequent since the Rudd government came to power.
Mr McMullan was one of the delegates at last week's high-level conference in Sydney on bilateral relations with Indonesia called "Australia and Indonesia: Partners in a New Era".
He says he wasn't aware of any discussion about Papua at the conference.
"We do air our differences, and we have a few, but we happily we have more agreements, we will continue to do that. We can only do in another persons country what they agree with, we don't allow other governments to do things in our country we don't agree with and vice-versa."
But Mr McMullan says they encourage Jakarta to continue going in the direction of giving Papua more autonomy.