Regulators are investigating the near-miss of two Qantas planes over Darwin last week, after an air traffic controller placed the two aircraft on the same flight path.
The Qantas planes, a Boeing 737 and a twin-engine Boeing 717, momentarily experienced a "loss of separation assurance" when the 717 was told to descend through the same level as the departing 737, the Australian Transport Safety Bureau said.
The 717 was on its way from Alice Springs, while the 737 was bound for Melbourne.
The near-miss was caused by an RAAF air traffic controller who has now been suspended. The RAAF shares air traffic control duties with civilian authorities in Darwin.
"An initial Defence investigation indicates that an air traffic controller inadvertently directed an arriving and a departing aircraft on a path that would have taken the aircraft through the same height," a defence spokeswoman confirmed.
"The aircraft safety systems identified the potential conflict and the air traffic controller immediately issued new instructions to separate the aircraft.
"In accordance with standard procedures, the air traffic controller concerned has been temporarily suspended from duty pending the results of [a more detailed] investigation."
The ATSB said an investigation was currently under way.
"There was no breakdown of separation standards," the ATSB said. "However a loss of separation assurance occurred."
Qantas confirmed the incident but noted that the Qantas-badged 717 was operated by Cobham, a flight contractor.
Qantas said it had no further comment as the investigation was still ongoing and is co-operating with the ATSB over the incident.
A separate near miss occurred in the Northern Territory between a Qantas 737 and an Air China A330 in April, when the planes converged flight paths at the same altitude during a shift handover between air traffic controllers.