Tony Abbott has declared he does not want illegal boat arrivals to dominate the Australia-Indonesia relationship and is aiming for the controversy surrounding his policies to deter people-smuggling to be only a "passing irritant".

"Indonesia is a land of promise for us and we do not want the relationship to be defined by boats," the new Prime Minister told The Weekend Australian yesterday. "This will hopefully be a passing irritant, not a long-term defining issue."

Preparing for his promised first overseas trip as Prime Minister to Jakarta at the end of next week, Mr Abbott played down the importance of the boats issue in the meeting with Indonesian President Susilo Bambang Yudhoyono. He also stressed the vital need for Australia to develop closer, more "intimate" ties with its nearest, largest neighbour.

Mr Abbott said he was ready to assist Indonesia with the issues that concerned it, including a broader agricultural relationship beyond just supplying live cattle and more two-way investment.

Advocating better, broader long-term ties with Jakarta, Mr Abbott said Australia should be heading in the direction of having a similar relationship with Indonesia as it has with New Zealand.

For months the Coalition's policy of using the Australian navy to turn people-smugglers' boats back into Indonesian waters has drawn criticism in Jakarta and in Australia, with Indonesian MPs complaining it would infringe national sovereignty.

When he returned as prime minister in June, Kevin Rudd suggested Mr Abbott's policy could lead to "armed conflict" with Indonesia and Julia Gillard taunted the then opposition leader in parliament, saying he did not have the "guts" to raise the issue with Dr Yudhoyono at a meeting in Darwin.

Mr Abbott this week spoke by telephone with Dr Yudhoyono and organised a precedent-setting first trip to Jakarta on September 30 and October 1.

Mr Abbott hopes all future incoming prime ministers will follow his lead and make their first official overseas trip to Indonesia as part of a move to get "more Jakarta and less Geneva" into foreign policy.

Mr Abbott yesterday responded emphatically to criticism that Australia would infringe on Indonesia's sovereignty. "We absolutely and fully respect Indonesia's sovereignty and wouldn't do anything to undermine it," he said.

"We want Indonesia's help and co-operation on this issue (illegal boat arrivals) and we are more than happy to be helpful and co-operative with Indonesia on the issues that are of concern to it."

Mr Abbott said boat arrivals "should never define our relationship and this trip is not all about boats". "Obviously it will be one element in the trip but, only one element and I want our relationship with Indonesia to be a stronger, deeper, broader relationship in the future than it has been the past. It's been a good relationship, mostly, but it's vital for our country that the relationship... be much more intimate in the years ahead than it has sometimes been in the past. It's probably not realistic to think of Australia having the same relationship as it has with New Zealand but that's the direction you would like it to move in."

Mr Abbott said Indonesia offered great opportunities for Australia. "We like to talk about how our coal and iron ore industries have benefited massively from the rise of China; I think Indonesia is now in a similar position economically to China in the early 80s and if we play our cards right this is a great opportunity for us," he said.

"The Indonesians would like to have a more broadly based cattle trade and more broadly based agricultural exchange than simply them buying our live cattle. Whether that involves more Australian investment in Indonesia or more Indonesian investment in Australia or both, I am obviously very open to it."

Mr Abbott, who was in Bali on holiday with his family during the second Bali bombings, said millions of Australians had spent happy times in the holiday destination and so "there is no reason why there can't be a much closer personal relationship that those millions of Australians feel for Indonesia and Indonesians".

"If Indonesia continues to grow at the current rate its GDP per head within a couple of decades will be at least that of Malaysia, at the present time, and by that time Indonesia's total GDP will be three or four times ours," he said.

"Even though the average Indonesian is likely to be poorer than the average Australian for a very long time to come, the strength of Indonesia will be vast and we need to ensure we are their trusted partners." Mr Abbott said the relationship was "in many respects our most important overall relationship".

Earlier this week, Mr Abbott tried to allay concerns raised by Indonesian MP Mahfud Siddiq that the Coalition's plan on illegal boats would contravene Jakarta's sovereignty.

Mr Mahfud, chairman of parliament's foreign affairs commission, said while Australia's handling of asylum boats in its waters was its legal prerogative, it had no authority to deal with them in international waters.