The Indonesian military is waiting for instructions on whether to cut co-operation with Australia in the wake of the spying revelations, including joint sea patrols aimed at combating people smuggling.
Jakarta is continuing to demand an explanation and an official response from Prime Minister Tony Abbott in relation to allegations Australian spies monitored the phone activity of the Indonesian president, his wife and some of his closest confidants.
Indonesian military spokesman Rear Admiral Iskandar Sitompul confirms that joint sea patrols are at risk as anger escalates in Jakarta over the spying drama.
"The joint patrol is aimed at catching migrants and handling other territorial issues," Rear Admiral Iskandar said.
The Indonesian Defence Ministry's director for international co-operation, Brigadier-General Jan Pieter, said he was still awaiting instructions from President Susilo Bambang Yudhoyono on whether to cut ties with Australia.
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Indonesian Law and Human Rights Ministry spokesman Marolan J. Barimbing also said preparations are under way to "lower the level of cooperation" with Australia in relation to anti-people-smuggling operations.
"Once there are instructions, we are ready to lower the level of co-operation," Mr Marolan told the Jakarta Post newspaper.
"We are anticipating such an instruction."
Indonesian ambassador to Australia, Nadjib Kesoema, was recalled from Canberra earlier this week in the wake of the spying revelations.
Indonesia is also continuing to insist on an official explanation from Australia after describing Mr Abbott's response to the drama and continued refusal to apologise as "regrettable".
"Australia, we need your answer," Dr Natalegawa said on Tuesday.
"This action is even illegal under Indonesia, Australia, or international law."
