The fighter jet crashed during a reconnaissance mission over northern Chad. But the pilot is alive after ejecting from plane, the officials said.
The pilot was later rescued, the ministry said in a statement.
His Mirage fighter jet crashed in an uninhabited region south of the town of Faya-Largeau, in the northeast of the country. No one on the ground was hurt in the crash.
The ministry said a "still unidentified accident" was behind the ejection and authorities were investigating.
France has more than 1,000 troops in Chad, a former French colony, protecting aid workers and providing communication and logistical support to the Chadian army.