Jakarta said it sought an explanation from Canberra after Indonesian police investigated a case in which the captain and crew of a migrant boat said Australian authorities allegedly paid them USD 31,000 to turn asylum-seekers back to Indonesia.
"With our goodwill, we ask for clarification and for further information on this issue. We did not received this," foreign ministry spokesman Arrmanatha Nasir told reporters.
Comments from the foreign ministry came after the Australian ambassador to Indonesia passed on a letter from his government on the issue to Indonesia's foreign minister Retno Marsudi, with Jakarta saying it gave no new details.
But Australia's ambassador Paul Grigson told reporters after the meeting that "Australian officials have always acted within the law in this case".
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"Australia remains very committed to cooperate with Indonesia to combat people smuggling in all of its forms," he added.
Nasir however questioned Canberra's commitment to addressing the people smuggling issue.
Relations between Jakarta and Canberra -- already tense after the recent execution of two Australians convicted of drug offenses in Indonesia -- have deteriorated since Prime Minister Tony Abbott refused to deny the allegations.
Indonesia has previously expressed disapproval of the tough immigration policy implemented by Abbott's conservative coalition after it came to power in 2013.
The policy includes turning back boats carrying migrants, mostly to Indonesia, and refusing to resettle asylum-seekers who arrive on unauthorised vessels even if they are found to be genuine refugees.