The asylum seeker boats issue will be but a "passing irritant" with Indonesia, Prime Minister Tony Abbott says.
Mr Abbott says Australia's relationship with Indonesia is strong and close and he wants it to be more so in the months ahead.
"The last thing that anyone should want is to have Australia's relationship with Indonesia defined by this boats issue which I am sure will be but a passing irritant," he told Fairfax Radio in Melbourne on Friday.
"That's one of the many reasons why it is so important to stop the boats, because I don't want what is in so many respects our most important relationship to be needlessly complicated by this."
The comments come after Indonesian foreign minister Marty Natalegawa warned that his country won't accept violations of its borders under the Abbott government's plan to turn back asylum seeker boats.
He said the move could damage relations between the two neighbours.
But Mr Abbott said Australia will work closely with Indonesia to stop the flow of boat arrivals in a way which fully respects Indonesia's sovereignty.
"We will do strong and sensible things which build on the strong relationship we already have with Indonesia," he said.
"It's in the interests of both countries that we stop these boats as quickly as possible."
Mr Abbott said there had been a "couple of hundred" asylum seeker arrivals on boats since the government was sworn in, but he didn't have exact numbers.
"The key change since the swearing in is now anyone who gets here illegally by boat is out of the country to Nauru or Manus within 48 hours and they're never coming back," he said.
The asylum seeker issue will be high on the agenda when Mr Abbott and Indonesian President Susilo Bambang Yudhoyono hold bilateral talks next week.
Interim Labor leader Chris Bowen said Mr Abbott's description of the issue as a "passing irritant" and Ms Bishop's lack of transparency about her meeting with Dr Natalegawa, showed poor judgment.
"It takes a special effort to endanger such an important bilateral relationship in the first week of office before Mr Abbott and Mr Yudhoyono have even met," Mr Bowen told reporters in Sydney.
Mr Bowen said Mr Abbott needed to distance himself from comments by former foreign minister Alexander Downer that the Indonesians were engaging in "pious rhetoric" over the boat issue.
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