Maltese PM Joseph Muscat confirmed that 109 passengers have been released from the flight.
He said some crew members are still present in the flight.
“Potentially 2 hijackers and some crew members still on board aircraft,” he tweeted.
The Libyan plane, carrying 118 people on board, was hijacked and then forced to land in Malta, media reports said.
The flight belongs to Afriqiyah Airways.
The flight was reportedly flying inside Libya when it was diverted to Malta.
The hijackers are reportedly armed with hand grenades.
Their demands are not yet known.
The deputy mayor for Lija in Malta, Madga Magri Naudi, told the BBC that paramedics and soldiers were standing by to see “what the next step is”.