In a dramatic escalation of the diplomatic tensions over border protection, Indonesia drew a line in the sand, saying it would step up its own maritime patrols.

After the Abbott government was forced to apologise over the incidents, Agus Barnas, the spokesman for the Co-ordinating Ministry of Political, Legal and Security Affairs, said the Indonesian government branded the incursions "a serious matter in bilateral relations".

"Indonesia demands that such operations conducted by the Australian government that led to these incidents be suspended until formal clarification is received and assurances of no recurrence of such incidents has been provided," he said.

"The government of Indonesia has the right to protect its sovereignty and territorial integrity in accordance with international laws and the charter of the United Nations."

Fairfax Media understands that three navy ships – including the heavily-armed frigate HMAS Stuart – and one Customs ship have crossed the 12-nautical-mile limit on a total of five occasions since December 13.

The incursions have raised questions as to whether the Abbott government's tough policies are pushing navy and Customs ships too close to the maritime boundary.

Sources told Fairfax Media there had been concerns raised that the Operation Sovereign Borders Joint Agency Taskforce – the border protection leadership – was ordering navy and Customs ships to positions too close to the maritime boundary in order to carry out the government's tough policies.

In some cases, ship commanders even raised questions at the time whether positions to which they were directed put them at risk of crossing the boundary.

One source said a review announced on Friday by Immigration Minister Scott Morrison would clarify whether border protection command and control was "playing too fine a line in positioning the ships too close to Indonesian waters".

Mr Barnas told a news conference in Jakarta on Friday afternoon that Indonesia "deplores and rejects the violation of its sovereignty and territorial integrity by the Australian vessels".

"The government of Indonesia underlines that any such violation on whatever basis constitutes a serious matter in bilateral relations of the two countries," he said. "Indonesia for its part will intensify its maritime patrols in areas where violation of its sovereignty and territorial integrity are at risk."

Mr Morrison and the head of Operation Sovereign Borders, Lieutenant-General Angus Campbell, refused to give details of the incursions.

One of the incidents is understood to have happened while an Australian ship was rescuing asylum seekers from their foundering vessel. But a recently retired navy captain, Lieutenant Commander Barry Learoyd, who served on border protection operations, told Fairfax Media at least some of the incursions had most likely happened while controversial boat turnbacks were being carried out.

"That's probably the only really plausible thing I can see happening ... If they'd inadvertently gone over the line, it would be because they've stopped, put their seaboats in the water and made sure these vessels are being pointed in the right direction and maybe the tide or the current has taken them over the line inadvertently."

Mr Morrison said the government had swiftly apologised to Jakarta. The Chief of Navy, Vice-Admiral Ray Griggs – who is known to have good relations with his Indonesian counterpart – also made a personal apology.

A defiant Mr Morrison insisted the government would stick with its tough approach. "We deeply regret the events. However, the Australian government remains committed to continuing to implement our policies to stop the boats," Mr Morrison said.

"There has been an inadvertent incursion into Indonesia's territorial sovereignty. That was not the policy of the government. This was actually in direct contradiction to the government's policy."

The Australian deputy ambassador, David Engel, conveyed the Abbott government's apology to Indonesia in a 35-minute meeting with a senior official in Jakarta late on Friday.

Mr Engel did not comment as he emerged, except to say: "I just had a constructive, cordial meeting, i conveyed the government’s apology ... Now I have to get back to the embassy and report back to my government".

Fairfax Media was seeking a response from Mr Morrison on Friday night but a spokeswoman said the minister was travelling and could not be reached.

smh.com.au