The Airbus A320 had been on a domestic Libyan route operated by Afriqiyah Airways from Sabha in the south to the capital Tripoli but was re-routed.
"The Afriqiyah flight from Sabha to Tripoli has been diverted and has landed in Malta. Security services coordinating operations," Prime Minister Joseph Muscat said on Twitter.
Libya confirmed the plane had been diverted.
Malta International Airport tweeted: "MIA confirms there is an unlawful interference at the airport. Emergency teams dispatched".
More From This Section
Maltese government sources told AFP that a single hijacker was on board and had told crew that he had a grenade. The hijacker said he would release the passengers as long as his as yet unspecified demands were accepted.
Libya has been in a state of chaos since the 2011 overthrow of Moamer Kadhafi left warring militias battling for control of different parts of the country.
Forces loyal to a fledgling national unity government recently took control of the coastal city of Sirte, which had been a bastion for the Islamic State group since June 2015.
A rival authority rules the country's far east, backed by the forces under military strongman Marshal Khalifa Haftar, who have been battling jihadists in second city Benghazi.