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Indonesian Foreign Minister Marty Natalegawa has revealed to Dateline there has been a lack of communication between the Australian and Indonesian governments over border and refugee issues.
"It often comes to our notice when such a policy takes place after the event," Mr Natalegawa said.
When asked about what advice Australia gives when sending boats back to Indonesian waters, Mr Natalegawa said, "we are somewhat caught by surprise to be honest."
The Indonesian Foreign Minister made the comments during an interview with Dateline’s Mark Davis.
"This is certainly not something that we really appreciate," Mr Natalegawa said.
"So far it’s been a very testing situation because we are seeing a policy that is often very difficult for us to be giving the impression of working hand in hand in unity."
The interview comes as the country prepares for elections in just over a month’s time and reveals the tensions over calls for Indonesia to be tougher on asylum seeker boats.
"It hasn’t been helpful obviously, any policies that give the impression of shifting the responsibility elsewhere - anyone but - creates problems," Mr Natalegawa said.
"But that’s really for Australians to judge ... to what extent such policy actually is consistent with Australia’s international commitments."
Australian Navy incursions into Indonesian waters have also tested the relationship with one of Australia’s most important neighbours.
"We want to ensure that there is no miscommunication and misunderstanding and that the issue doesn’t get out of hand," he said.
"I am in regular contact with Minister Bishop, I spoke to her just now on a number of issues, so it’s very, very important to have these communications established."
Relations were also recently strained by revelations over the surveillance of President Susilo Bambang Yudhoyono.
"Some [issues] to be fair is not of the current government’s making, after all the issue of surveillance is not something that just happened overnight, it’s apparently a long-established practice," Mr Natalegawa said.
And he’s sure that the links between the two countries are improving again ahead of a potential change in government in Jakarta.
"I think we are now back on the upward trajectory, you are quite correct we’ve had a somewhat difficult time recently, but both governments are working earnestly and with a great deal of urgency to try to get the relationship to back where it was before.
"I am keen to ensure that when the baton is passed from this government to the next, it will be passed where Indonesia and Australia relations is already back on track, so we must ensure that the situation gets managed quickly."