The Air North plane had taken off from Darwin Airport and then crashed at the nearby RAAF base about 10.20am (CST) on Monday, police in Darwin said.
Police are notifying the next of kin of the two crew members killed.
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A spokesman for Air Services Australia in Canberra said the incident involved an Embraer 120 aircraft, a Brazilian-made twin-engined commuter airliner used by a number of Australian regional airlines.
"There was an aircraft crash at Darwin this morning. That incident is continuing," he said.
"We don't believe there were any passengers on board, which is good news."
Air Services aviation rescue and fire personnel were currently on the scene, assisted by Northern Territory emergency services.
