Indonesia says it will reject key parts of Prime Minister-elect Tony Abbott's asylum seeker boat policy, in a blow to the incoming Coalition government.

Indonesia's foreign minister Marty Natelegawa told a meeting of his parliament's foreign affairs commission that Mr Abbott's "policy about people smuggling" was a "problem" that Indonesia had to manage.

He said Indonesia would have to differentiate between the political campaign Mr Abbott was trying to win and what the reality would be once he is sworn in.

But Mr Natelegawa told the commission that Indonesia would reject Mr Abbott's policy of buying boats from Indonesian fishermen.

"Clearly we will reject it if they say they will try to prevent any boat from sailing from Indonesia to Australia by buying boats from our fishermen," Mr Natelegawa said.

During the election campaign the Coalition pledged to buy back unseaworthy boats from Indonesian villagers as part of its regional action plan against people smuggling.

The policy was slammed as "clumsy" and "crazy" by then immigration minister Tony Burke, and .

"It will make Indonesia-Australia relations sour because, of course, Indonesia will not readily accept what is proposed by Australia," Professor Juwana of the University of Indonesia said last month.

Mr Natelegawa also told the meeting that the Indonesian government rejected Australia becoming involved in "early detection" methods or violating Indonesia's sovereignty.

Mr Abbott proposed, during the election campaign, that millions of dollars be set aside to pay Indonesian villagers to give information to Australian authorities about people smuggling movements.

"Hopefully in the next couple of days when we start communicating, we can find out the exact policy," Mr Natelegawa said.

"But for sure, we will reject it if there are policies that are not in line with the spirit of partnership and [Indonesia's] sovereignty and national integrity."

Mr Abbott announced Operation Sovereign Borders in July, setting out a military-led response to fight people smuggling, led by a three-star commander.

The response will also turn back asylum seeker boats when safe to do so, a policy not supported by Indonesia.

President Susilo Bambang Yudhoyono and Mr Abbott held their first phone conversation since the election on Tuesday.

The two leaders will meet at the APEC summit in Bali early next month, however it is possible Mr Abbott will visit Jakarta earlier to discuss regional issues and strengthening bilateral relations.

Mr Abbott has said he is confident of working through any issues with Indonesia.