Australia had been “stupid” to allow its navy ships to cross into Indonesian territory, and tension over the incident would delay the process of repairing relations damaged by recent spying revelations, according to a senior Indonesian politician.

Meanwhile, Australia's Chief of Navy, Vice-Admiral Ray Griggs, has hit back at claims of misconduct by Australian sailors in the past fortnight, insisting his personnel were "worthy of more respect than has been shown to them in the past few weeks".

Indonesian politician Tantowi Yahya, a member of the Parliament's foreign affairs commission, has said he was sceptical about Immigration Minister Scott Morrison and Foreign Affairs Minister Julie Bishop's insistence that the territorial breaches during the government's boat turn-back operations were “inadvertent”.

“Australia is stupid to do that. I think there was no way that they did not know they had crossed the border. They have more sophisticated navigation equipment than ours. How come they didn't know they had entered Indonesian waters?” he asked.

Mr Tantowi agreed with the Coordinating Minister for Security, Djoko Suyanto, who said last week that the incident would prolong the existing dispute between the two countries over spying allegations, which led to Indonesia recalling its envoy to Australia for the past eight weeks.