Ties between the neighbours sank to their lowest point in years in November after reports that Australian spies tried to tap the phones of President Susilo Bambang Yudhoyono and his inner circle.
Jakarta recalled its ambassador from Canberra and suspended cooperation in several areas over the incident, including efforts to stop people-smuggling boats reaching Australia.
Yudhoyono called for a code of conduct to govern behaviour and, after months of talks on the issue, Australian Foreign Minister Julie Bishop and her Indonesian counterpart Marty Natalegawa today signed an agreement.
In the agreement, Indonesia and Australia pledge to not use their intelligence agencies to harm one another and to increase cooperation at a time fears are growing about the threat posed by home-grown Islamic militants returning from Middle East conflicts.
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"We are back to where we should have been in terms of Indonesia-Australia relations," Natalegawa said, adding that he believed cooperation would be "even more enhanced in the future in front of us".
She added the agreement was "the most effective way to defeat those who would do harm to the people of Australia and Indonesia".
Both countries have expressed alarm that home-grown extremists are heading in increasing numbers to fight with violent groups such as the Islamic State overseas, and have stepped up counter terrorism efforts.