"While carrying out its operation in Hombori region, Mirage 2000D met with an accident that required crew ejection," the ministry said.
Two men were on board, with one of them having got minor injuries and transferred to the Gao base in northern Mali, the statement read.
The jet debris were detected by forces of counterterrorist Operation Barkhane. An investigation will be opened to determine the causes of the crash, the ministry added.