Australia's rescue operations within the territorial waters of Indonesia will soon be governed by a formal agreement between Canberra and Jakarta, a top official of the Indonesian government hinted late Wednesday.

According to Indonesian Defence Minister Purnomo Yusgiantoro, a bilateral deal would be finalised between Australia and Indonesia on September, which would allow the Australian navy to enter Indonesian waters during distress calls from vessels attempting to reach Australia.

Planes dispatched by Australian authorities would also be given unhindered access within the same emergency situations, Mr Yusgiantoro said.

Effectively, the two-nation arrangement would simply recognise what the Australians have been doing, the Indonesian official pointed out, "but actually they're doing it without rules protecting them."

The Indonesian disclosure was made following the one-on-one discussion between Prime Minister Julia Gillard and Indonesian President Susilo Bambang Yudhoyono in Darwin on July.

In an earlier statement, Home Affairs Minister Jason Clare described the meeting between Ms Gillard and Mr Yudhoyono as exploratory talks that aim to improve on the exiting cooperation between Australia and Indonesia regarding the boat people affair.

"(The meeting) agreed to look at additional ways to strengthen search and rescue capabilities, including possibly the provision of technology for Indonesia's search-and-rescue agency (BASARNAS)," Mr Clare was reported by The Daily Telegraph as saying.

The cabinet minister, however, downplayed the reported imminent deal on the issue as described by Mr Yusgiantoro by clarifying in a statement that "this particular proposal has not been put formally to the government and has not been under consideration."

But Mr Clare did not deny that he and Defence Minister Stephen Smith were due to visit Indonesia on August purportedly to confer with their local counterparts, creating a scenario that is akin to Indonesia's claims.

On Thursday, Indonesian Foreign Minister Marty Natalegawa backed the statement of his cabinet colleague by confirming that talks between Canberra and Jakarta were indeed underway and they mostly they delve on determining the specific protocols that would guide the entry of Australian ships into Indonesian waters.

A statement by his ministry alluded to the meeting last month between Ms Gillard and Mr Yudhoyono, which apparently had intended to pick up on the current set ups that were the basis of Australia's rescue mission behaviour while operating in Indonesia.

"The joint communiqué issued in Darwin said both countries will advance co-operation. It means we will start from something that we already have, we will not start a completely new co-operation," The Sydney Morning Herald reported the ministry statement as saying on Thursday.

However, the Indonesian statement did not touch on the processing aspect of the upcoming deal between the two governments, leaving more questions on where the asylum seekers plucked out by the Australian navy from Indonesian waters would be taken for proper handing.

Yet the same Fairfax report has indicated that Australia had agreed to take on the processing role as another Indonesian official allowed: "Based on the understanding (between the two countries), rescued people will be brought to the rescuers' country.

That decision was based on the premise that Australia is more capable of responding to distress calls sent out by boats carrying asylum seekers as compared to Indonesia, the same official told The Herald.