Jakarta is not aware of any other cases where Australia has paid people smugglers to "re-traffick" asylum seekers.
There are claims Australian officials also paid off people involved in smuggling under the Labor government, but Indonesia's Foreign Ministry spokesman Arrmanatha Nasir says this is the first time an Indonesian police investigation had turned up such information.
"This is the first time that we know of such an incident where smugglers were given money by a foreign government to redirect or to re-smuggle or re-traffick their passengers," he told reporters in Jakarta on Thursday.
A boat captain and five crew members held in Rote for aiding 65 people who wanted asylum in New Zealand say an Australian official paid them cash to turn back to Indonesia.
Indonesia's foreign minister asked the Australian ambassador to explain the situation on Saturday, but has not received an answer.
Mr Nasir says Indonesia doesn't need Canberra's response for its police investigation.
"It's not that the answer is not important," he said.
"The (investigation) process for the captain and crew won't need to wait for the answer because there's other evidence that can be used."
The group was being investigated over people smuggling, not for accepting the cash, he said.
Mr Nasir said the reply from Canberra was also less important in the bigger picture of stopping people smuggling.
"When we ask for clarification, certainly we hope that clarification will be given," he said.
"This is not an exact science.... This is the process and procedure of diplomacy."
Indonesia wanted co-operation with Australia on people smuggling, Mr Nasir said.
It was committed to the Bali Process and hoped all countries would work together.
"We want to encourage all countries to address this issue in a comprehensive manner, that's the issue," he said.
"It's not about punishment, not about sanctions."
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