An investigation is under way and a Defence air-traffic controller is being suspended after two Qantas aircraft came within seconds of colliding over Darwin last week.
The two planes packed with passengers, one heading to Melbourne and one arriving from Alice Springs came within 250m of each other on Tuesday last week, the NT News reports.
The Department of Defence, which controls air traffic at Darwin Airport, told AAP that an initial investigation indicated an operator inadvertently directed an arriving and a departing aircraft on a path that would have taken them through the same height.
"The aircraft safety systems identified the potential conflict and the air-traffic controller immediately issued new instructions to separate the aircraft," it said in a statement.
Defence said the air-traffic controller concerned had been temporarily suspended, pending the results of an investigation.
The NT News reports a traffic collision-avoidance system on board the plane from Alice Springs warned the other plane was just 247m below.
But one of the pilots said "it must have got a lot closer than that", the newspaper said.
The Australian Transport Safety Bureau is investigating.
A Qantas spokeswoman said she would not comment on the incident while the investigation was ongoing.
"Safety is our number one priority," she said.