Indonesia says it will raise the Abbott Government's asylum seeker policy with the United States during official talks next week.

Jakarta has stepped up its protest to the Coalition's boat turn-back policy, calling in the Australian ambassador in Jakarta for a meeting with a senior official.

Indonesia's foreign affairs minister Marty Natalegawa says a strong protest message was given to Australian ambassador Greg Moriarty over the use of lifeboats to send asylum seekers back.

Dr Natalegawa says Australia was already violating its international commitments, but the use of lifeboats to send people back is an escalation.

"What Australia has been doing is a bigger development than before," he said.

"In the past when they have turned back the boats, or pulled the refugee boats back to Indonesia, that alone is a violation against their international commitment under the Refugee Convention.

"But this time it has escalated."

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Dr Natalegawa told reporters Indonesia does what it can to stop boats leaving the country and that Australia's actions are "against the values of humanity".

He says he will inform US secretary of state John Kerry - who will visit Jakarta next week - about Australia's actions and let officials draw their own conclusions.

"There is no need to ask; we only need to inform it, and let America draw its own conclusion," he said.

Dr Natalegawa says he will discuss Australia's policy with other countries as well.

Australia, Indonesia relationship 'very positive': Bishop

Foreign Minister Julie Bishop says the asylum seeker issue is raised when she speaks with Dr Natalegawa but their relationship remains positive.

"We have open lines of communication and I'm constantly talking to Dr Natalegawa," she said.

"I think he said recently that we talk almost every day. It's a very positive relationship - of course we have challenges.

"Neither of us want to be in a position where we have to deal with the people smuggling trade."

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Opposition immigration spokesman Richard Marles says calling in Mr Moriarty is a "very grave step to take".

"Now we have a circumstance where the kind of cooperation which actually existed in terms of reducing that flow of boats under Labor has ceased and we have a situation where the policies of this Government in relation to this issue has led to our ambassador being called in before the foreign minister," he told the ABC's Lateline program.

"We should be working effectively together between Australia and Indonesia; the truth is we're in a period now where there is precious little cooperation at all.

"The calling in of an ambassador by a foreign minister is a very grave step to take."

Opposition foreign affairs spokeswoman Tanya Plibersek says it is clear the ambassador received a dressing down.

"I think it's of enormous concern that a huge nation, a growing democracy right on our doorstop, a nation that's vital to our security but also our economic prosperity is now in open conflict," she said.

Earlier this month Dr Natalegawa said it was "unhelpful" to bilateral relations for Australia to keep pursuing its policy of turning back asylum seeker boats.

He made the comments after the Australian Government said it had entered Indonesian waters without permission while trying to stop the arrival of the vessels.

Immigration Minister Scott Morrison blamed the incursions on "positional errors" and said the Government took its "shared commitment with Indonesia to mutually respect the sovereignty of each nation very, very seriously".

This prompted Indonesia to beef up naval patrols, although Dr Natalegawa played down suggestions the country was going on a war footing, saying they needed to ensure "things don't get out of hand".

Prime Minister Tony Abbott has said his Government is committed to continuing the policy of turning back boats, and lifeboats are now being used to send asylum seekers rescued from unseaworthy vessels back to Indonesia.

In January, the Government said the number of asylum seekers arriving by boat in Australia had fallen by 80 per cent since Operation Sovereign Borders was introduced four months ago.