Lake Evella Airport emergency services were on scene shortly before 1pm but it is understood there were no injuries.
A NT Police, Fire and Emergency Services spokeswoman said while details were scant, it appeared the plane had overshot the runway.
The airport is located in northeast Arnhem Land, about 500km east of Darwin and 120km west of Nhulunbuy.
The near miss comes after a catastrophic light plane crash claimed the lives of two pilots in Darwin’s rural area in October last year.
That incident remains under investigation by the Australian Transport Safety Bureau but it is believed that landing gear on the Fly Tiwi charter from Darwin did not lower correctly.