Mr Abbott told a media conference on the Indonesian island of Bali that anti-Indonesian protesters were not welcome in Australia.
The prime minister also claimed the situation in West Papua was getting better with greater autonomy for the people and praised President Susilo Bambang Yudhoyono for ensuring a better level of government services and imrpoving conditions in the restive provinces.
Mr Abbott claims consular staff spoke to the protesters before they left the Bali consulate.
Speaker:Tony Abbott, Australian Prime Minister
TONY ABBOTT: Consular staff as I understand it had a very lengthy discussion with them and after that very lengthy discussion, they agreed to leave. That, as I understand it, is the fact of the matter.
Now, I want to make two fundamental points and I want to stress these points, I want to put them up in flashing neon lights, I want to underline them. One, Australia will not give people a platform to grandstand against Indonesia. We have a very strong relationship with Indonesia and we are not going to give people a platform to grandstand against Indonesia. I want that to be absolutely crystal clear. And people seeking to grandstand against Indonesia, please don't look to do in Australia. You are not welcome.
Second point I make is the situation in West Papua is getting better not worse and I want to acknowledge the work that President Yudhoyono has done to provide greater autonomy, to provide a better level of government services and ultimately a better life for the people of West Papua.
The other point I should make is that Australia absolutely respects the territorial integrity of Indonesia and while I acknowledge the right of people to free expression. I acknowledge the right of people to fair treatment under the law. I should also make the point that the people of West Papua are much better off as part of a strong, dynamic and increasingly prosperous Indonesia.