The Malawi Defense Force aircraft "went off the radar" after it left the capital, Lilongwe, on Monday morning, it added.
The president ordered a search and rescue operation after aviation officials were unable to contact the aircraft, the BBC reported.
It was supposed to land at Mzuzu International Airport, in the country’s north, just after 10:00 local time (11:00 BST)
After being informed of the incident, Malawi's President Lazarus Chakwera cancelled his scheduled flight to the Bahamas.
MNA