A senior officer from the Indonesian navy has called for Australia to abandon its plan to turn back boats with military force.
Canberra has announced the new policy in a bid to stop asylum seekers from reaching Australia by boat.
Those intercepted at sea will be sent to Australia's detention centres in Papua New Guinea and Nauru for processing, and should they be declared refugees they will be settled outside Australia.
The foreign ministry in Jakarta says the plan to turn back asylum seeker boats will risk cooperation and trust in joint efforts aimed at combatting people smuggling.
The Australian foreign minister, Julie Bishop, has said the government will not be seeking permission to implement its asylum seeker policies despite Jakarta labelling some of the measures as an attack on Indonesian sovereignty.