Indonesia's top military commander has reportedly accepted that Australia's recent incursions into the country's waters were accidental, paving the way for reduced tensions between Canberra and Jakarta.

Despite some fiery rhetoric in Jakarta and even accusations that Australian Navy and Customs ships knew they were breaching Indonesian sovereignty, the chief of the country's armed forces, General Moeldoko, has said the incursions were mistakes, according to the Jakarta Post.

''[What has happened recently] was accidental, but we will always be alert in protecting our borders,'' he is quoted as telling the Indonesian parliament's foreign affairs and defence commission.

He was reportedly hosing down accusations by some parliamentarians that Australia's breaches were designed to disrupt Indonesia's coming elections.

Fairfax Media understands there were about five breaches in December and January while Australian Navy and Customs ships were carrying out border protection operations – at least some during boat turn-backs, which Jakarta opposes.

General Moeldoko is known to be close to the Chief of the Defence Force, General David Hurley. General Hurley received an interim report into the causes of the breaches recently.

It is understood that this inquiry has found that navigational errors were made both by Operation Sovereign Borders headquarters as well as the ships themselves. But it is not clear whether a full explanation of the breaches will be made public once the full report has been completed.

Indonesia's initial reaction when the Abbott government admitted the breaches was one of fury, with Jakarta vowing to move a frigate down to its southern waters to boost patrols.

Immigration Minister Scott Morrison and other senior government figures swiftly apologised for the ''inadvertent'' breaches.

Foreign Minister Marty Natalegawa said such incidents as well as Australia's tough border protection policies more generally were ''complicating'' efforts to return relations to normal in the wake of revelations that Australia spied on senior Indonesian politicians.