Patrick Walters – Alexander Downer will meet senior Indonesian officials today in a bid to calm Jakarta's concerns over Australia's handling of 43 Papuan asylum-seekers now on Christmas Island.

There is a growing expectation in Canberra that most, if not all, of the 43 could end up staying in Australia after having their cases examined by the Department of Immigration.

The issue is extremely sensitive for the Yudhoyono Government, with senior Indonesian officials warning recently that conferring refugee status on the Papuans would undermine bilateral relations with Canberra.

"Their applications are being considered one by one by the Immigration Department and they will make an assessment consistent with the legal obligations that Australia has," Mr Downer said yesterday ahead of leaving Australia for Jakarta.

The Foreign Minister will have breakfast with his counterpart, Hassan Wiryuda, this morning at the start of a 16-hour visit to the Indonesian capital.

Mr Wiryuda raised the Papuan case in a recent telephone call with Mr Downer following a similar call from President Susilo Bambang Yudhoyono to John Howard last month. A grant of asylum by Australia would confirm in the minds of some Indonesian policy-makers that Canberra was seeking to undermine Indonesian sovereignty over West Papua and encourage secessionist sentiment.

Immigration officials have interviewed all the group who landed near Weipa, in northern Queensland, after a five-day canoe voyage. The department will make a final assessment on their applications by mid-April.

Dr Yudhoyono personally guaranteed to the Prime Minister that the asylum-seekers would not be harmed if they returned to Indonesia.

Dr Yudhoyono and Mr Wiryuda say that Indonesia has steadily improved its human rights record in West Papua.

The 43 Papuans, who included independence activists, say they could be killed or persecuted if they are forced to return home – a claim rejected by Jakarta.

Mr Downer will also discuss strategies for curbing illegal fishing in Australian waters by Indonesian fishing vessels and raise the issue of clemency for Bali Nine ringleaders Andrew Chan and Myuran Sukumaran – sentenced to death by a Bali court two weeks ago – with Mr Wiryuda.