Foreign Minister Julie Bishop has personally apologised to her Indonesian counterpart, Dr Marty Natalegawa, over revelations Australian ships repeatedly breached Indonesian territorial waters in asylum seeker operations.

Indonesia said on Friday it would send a navy frigate to bolster its southern defences, and demanded Australia immediately stop turning asylum seekers' boats back to its territory.

In Perth, Ms Bishop confirmed she had contacted Dr Natalegawa to express Australia's regret for its actions.

"I have contacted him in writing," Ms Bishop said.