Australia and Indonesia will work together to rehabilitate hundreds of convicted terrorists expected to be released from Indonesian prisons in the coming years.

Addressing a high level counter-terrorism meeting hosted by the United States Secretary of State, John Kerry, on the sidelines United Nations General Assembly in New York, Foreign Affairs Minister Julie Bishop said Australia and Indonesia would hold a conference next month on the threat posed by convicted terrorists who will soon finish their sentences.

"We are aware that in the coming years a significant number of prisoners in Indonesian prisons who have been convicted of terrorist related activities will be released, it runs to the hundreds, and of course if they have not been rehabilitated then they pose a serious risk, not only to our country but to our region," Ms Bishop said after the meeting.

During the meeting of the Global Counter-Terrorism Forum, both Mr Kerry and Ms Bishop urged the international community to step up its efforts against the threat of foreign fighters.