The ministry's online newspaper said the Russian-made MiG-21 aircraft crashed inside al-Annad air base in the southern province of Lahj due to technical failure.
It said the jet's pilot, Col. Atiq al-Akhali, was killed and a trainee was injured.
Ansar al-Shariah, a group affiliated to al-Qaida in Yemen, had named al-Akhali and 11 other pilots in a hit list, promising to pay anyone who killed them a reward of around $5,000. The list, which was circulated on militant websites in June 2011, came as the Yemeni Air Force was carrying out aerial strikes against al-Qaida militants in the south. The group had seized control of large swaths of territory in southern Yemen during last year's turmoil against the country's longtime authoritarian leader. The military took back control earlier this year.
Al-Annad in Lahj is the biggest air base in the country. It hosts a group of U.S. military advisers helping Yemeni troops fighting the local branch of al-Qaida, considered by the U.S. to be the terror network's most dangerous offshoot.
Meanwhile, a Yemeni court sentenced six al-Qaida militants to up to five years in prison over planning attacks and targeting security forces, foreign interests and state institutions. Heavy security forces were deployed to the court building in Sanaa.
A total number of 12 defendants were tried on charges of "forming armed groups to carry out criminal acts" and "planning attacks on military and government buildings and private and public property, including foreigners and the U.S. Embassy and other diplomatic missions in Yemen," between 2009 and 2011.
Six were acquitted while six others received sentences varying between one to five years in prison.
The trial comes at a time Yemeni President Abed Rabbo Mansour Hadi has ordered trials for tens of al-Qaida suspects, who are among hundreds of suspected extremist militants that have been held without charges for over a year.