The incident took place Wednesday morning, 18km south southwest of Daly River.
NT Police have confirmed the aircraft was taking part in Exercise Pitch Black.
An unconfirmed social media report said it was an aircraft from the Italian Airforce.
The pilot ejected from their aircraft during flying operations and made immediate contact with aircrew in the area through radio.
“Australian Defence Force personnel responded immediately and professionally at 10:45am to an aircraft emergency in the exercise area,” a statement said.
“They coordinated recovery of the pilot with a search and rescue helicopter.”
The pilot arrived at hospital at 1.30pm for precautionary checks, but is otherwise safe and well.
The Australian Defence Force has confirmed all flying had been cancelled for the remainder of Wednesday.
The Pitch Black exercise is the largest in its 43-year history with about 140 aircraft and more than 4000 personnel from 20 nations taking part.
Participants include Italy, who are making their Pitch Black debut this year, France, the United Kingdom and the United States.
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