Air-safety investigators are looking into a close shave between Singapore Airlines and Jetstar passenger jets over the Northern Territory on Thursday afternoon.

The Singapore Airlines A330 aircraft was flying from Brisbane to Singapore when an air-traffic controller cleared the Jetstar A320 to climb through the larger plane’s cruise level, which resulted in a so-called "loss of separation".

The Jetstar plane was flying from Darwin to Brisbane.

The Australian Air Transport Safety Bureau said the incident occurred about 75 kilometres east-south-east of Tindal in the Northern Territory. The air force has a base at Tindal, which is near Katherine.

The bureau has not revealed how close the planes came to each other, and will not release a final report into the incident until November.

A "loss of separation" occurs when two aircraft fly within 305 metres vertically and 9.26 kilometres on a horizontal axis of each other, raising the risk of collision.

Following a spate of high-profile incidents, last October the ATSB released a 114-page report into "loss of separation" cases between June 2008 and June 2012.

The bureau raised concerns in the report about the "relatively high" number of aircraft that have flown too close to one another in the country’s military-controlled airspace.

While Airservices Australia monitors the bulk of this country’s airspace, the Department of Defence oversees both civilian and military aircraft in airspace at Darwin, Newcastle and Townsville.

The ATSB pointed out in the report that most of the incidents in military-controlled areas were the "result of controller actions", and Darwin and Williamtown in Newcastle were "in particular over represented".

The bureau’s report showed that a loss-of-separation incident between planes under air traffic control in Australia occurs on average once every three days.

However, the ATSB emphasised in its report that the rate of near misses due to civilian air traffic control was one of the lowest in the world.

In almost 90 per cent of cases, the bureau said there "was no or a low risk of aircraft colliding", while only about six cases a year "represent an elevated safety risk".