Indonesia's government and military are closing ranks against Australia's policy of turning back asylum seeker boats, after claims two boats were recently forced back to Indonesia.

The Indonesian president's office has backed his foreign minister's rejection of Australia policy, saying turning boats back to Indonesia is "unhelpful".

And Indonesia's military chief General Moeldoko, who was quoted in the Jakarta Post as saying he had "agreed" to Australia's policy, now says his words have been "twisted".

Earlier this week General Moeldoko was reported as saying that his Australian counterpart, General David Hurley, called him to explain that Australia would be turning boats back.

"I have agreed. Therefore, we don't need to feel offended," The Jakarta Post reported him as saying.

But General Moeldoko now says he does not support Australia sending asylum seeker boats back to Indonesia.

He says his words merely meant that he recognised the Australian Navy was carrying out orders from the Federal Government

"My response was not approving it. I said 'I understand the tactical steps,' that's my standpoint," he said.

He says the Indonesian military, or TNI, always follows the government's policy and cannot have its own view.

"I reflect to myself that if the job was given to me by my government, I would have done the same, so that is the context," he said.

"I did not speak about foreign policy, instead I spoke about tactical decisions in the field. My statement should not be twisted."

The general blamed misreporting and told journalists to "straighten it up".

His comments come after passengers from two asylum seeker boats were found on an Indonesian island saying they were forced back by the Australian Navy.

Some of the asylum seekers say they were mistreated by Australian personnel and their boats were abandoned in rough seas after being taken back to Indonesian waters.

Indonesian politician says military won't allow Australia to send asylum seekers back in lifebaots

Meanwhile, a senior Indonesian government source has also criticised reports of an Australian Government plan to use powered lifeboats to help get asylum seekers back to Indonesia.

Mahfudz Siddiq, the chairman of Indonesia's Foreign Affairs Commission, has questioned the difference between that and people smuggling syndicates providing boats.

"The Australian Government action, by returning the two boats back to Indonesia, is a provocative action," he said.

"Instead of solving problems, it will trigger more conflict, it will have an impact broadly and fundamentally on the bilateral relations, it will cost both countries."

He says such action would not be tolerated by the Indonesian military, adding that were the rescue boats to re-enter Indonesian waters, "this becomes a smuggling operation, legalised by the Australian Government. This of course would not be accepted by Indonesian military, because it has been a defence issue and breaching water territory sovereignty."

Abbott defends silence on asylum seeker policy

Yesterday Prime Minister Tony Abbott defended the Government's refusal to release details about asylum seeker policies.

"I'd rather be criticised a bit for being a bit of a closed book on the issue, and actually stop the boats," he said.

"I'm pleased to say that it's now several weeks since we've had a boat, and the less we talk about operational details on the water, the better when it comes to stopping the boats."