Indonesia’s incoming president has issued a blunt warning to Tony Abbott that it’s unacceptable for the Australian navy to enter Indonesian waters uninvited while turning back asylum seeker boats.

President-elect Joko Widodo said Australia and Indonesia have closely overlapping strategic interests but he promised a tough approach to issues of sovereignty.

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The former Jakarta governor outlined plans to strengthen ties, including boosting military and intelligence links.

But he warned he would be “stronger” on questions of sovereignty, even than his army-general election opponent, Prabowo Subianto.

Mr Joko raised concerns about Australia’s asylum seeker policies and warned against Australian naval vessels venturing into Indonesian waters without permission as they did on five occasions last year.

“We will give a warning that this is not acceptable,” he said.

“We have international law, you must respect international law.”

Bilateral relations were damaged by revelations of Australia’s naval incursions and its spies tapping the phone of outgoing president Susilo Bambang Yudhoyono’s wife.

But Mr Joko said he would rebuild security ties, including cooperation to combat terrorism.