Immigration Minister Scott Morrison has hailed Australia's hardline asylum seeker policy as a blessing for incoming Indonesian President Joko Widodo and his nation.

As Prime Minister Tony Abbott prepared to fly to Jakarta for Mr Joko's swearing in ceremony on Monday, Mr Morrison responded to the new president's warning that he would not tolerate Australia entering Indonesian waters in pursuit of towbacks and turnbacks of asylum seeker boats.

Australia admitted and apologised for a number of naval incursions earlier in the year as part of secretive operations to stem the flow of asylum seekers between Java and Christmas Island.

"We will give a warning that this is not acceptable … you must respect international law," Mr Joko told Fairfax Media in his first interview with an Australian media outlet.

Early signs are that Mr Joko will take a harder, more nationalistic approach to the diplomatic relationship than the outgoing Susilo Bambang Yudhoyono.

But Mr Morrison appeared to push back, saying Operation Sovereign Borders had benefited Indonesia as it had Australia.

"As a result of Operation Sovereign Borders, Indonesia and Australia are no longer faced with the people smuggling curse that ran rampant during the Labor years, sending almost 1200 people to their deaths, often just off the coast of Java," he said.

"The incursion incidents referred to [by Mr Joko] were inadvertent and were addressed with the previous administration.

"It was not the policy then of the Australian government nor is it our policy now to enter Indonesian territorial waters in relation to Operation Sovereign Borders operations."

But Labor's deputy leader and foreign affairs spokeswoman Tanya Plibersek cast doubt on Mr Morrison's robust assessment of the Indonesian relationship and the benefits of turnbacks, describing Mr Joko's statements as "very telling indeed".

"It is clear that President Joko Widodo is very concerned about the way the Australian government has been making announcements about what is going to happen on Indonesian soil and Indonesian waters without ever having discussed it with the Indonesian government, and is very concerned about the six or so incursions into Indonesian waters by Australian naval vessels in the last year," she said.

"It is not surprising that the new President of Indonesia is sending a very strong message to Tony Abbott that the President of Indonesia sees the sovereignty of Indonesia as a very important issue for him.

"This certainly shows that despite the claims that Tony Abbott has made, the relationship with Indonesia has not been repaired. It is not in the healthy state that it was before Tony Abbott came into government and there is still a repair job to be done."

In a weekly message to be released on Sunday, Mr Abbott did not mention the boats issue but described Indonesia as a "hugely important neighbour" and restated his aim to increase trade and deepen ties.

"On present trends, Indonesia will be the fourth biggest economy in the world by mid-century," he said. "Yet despite this, two-way trade with Indonesia is only $15 billion.

"In fact, our two-way trade with New Zealand, with just four million people, exceeds our current two-way trade with Indonesia and its 250 million people."

"The outgoing President, President Yudhoyono, has been a great friend of Australia.

"Australia wants the new President to succeed – because a strong, prospering, democratic Indonesia has so much to offer the world."