The international aircraft was taking part in the biennial Exercise Pitch Black training event when it crashed near the Northern Territory's Daly River on Wednesday morning.
Defence Minister Richard Marles' office confirmed the pilot ejected from the aircraft before the crash, with no fatalities reported from the incident.
The pilot was taken to the Royal Darwin Hospital in a stable condition for precautionary checks, but police said they were "otherwise safe and well".
A Defence spokesperson said a search and rescue helicopter had helped to recover the pilot.
"The exercise participant made immediate contact with air-crew in the area via radio following their ejection," the spokesperson said.
"The pilot arrived at hospital by helicopter around 1:30pm (local time).
"All flying for the remainder of the day has been cancelled. Defence will provide further updates when available."
It is not yet known what type of aircraft was involved in the crash, or what caused the incident.
Pitch Black, one of the largest tactical air operations in the world, is hosted by the Australian Royal Air Force and includes 20 countries, more than 140 aircraft and 4500 personnel.
The exercise is being held out of both the RAAF Base Darwin and RAAF Base Tindal.
The Air Force's website describes the operation as its "most significant flying activity for strengthening international engagement and enhancing our ability to work with overseas partners".
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