The hijacker told crew he was "pro-Gaddafi" and that he was willing to let all 111 passengers leave the Airbus A320, but not its seven crew, if his demands were met, Reuters reported.
It was unclear what the demands were or whether the hijacker was acting alone.
Libya has been dominated by violence since a NATO military intervention followed the 2011 uprising that led to the overthrow and death of the country's long-time dictator, Muammar Gaddafi. Rival governments were set up in Tripoli and eastern Libya back in 2014.
Troops took up positions a few hundred meters (yards) from the plane as it stood on the tarmac and no one was seen boarding or leaving it. The aircraft's engines were still running 45 minutes after it landed in late morning, the Times of Malta said.
All other flights at Malta International Airport were canceled or diverted, it said.
The aircraft had been flying from Sebha in southwest Libya to Tripoli for state-owned Afriqiyah Airways, a route that would usually take a little over two hours.
The tiny Mediterranean island of Malta, a European Union member, is about 500 km (300 miles) north of Tripoli.
Maltese Prime Minister Joseph Muscat tweeted: "Informed of potential hijack situation of a #Libya internal flight diverted to #Malta. Security and emergency operations standing by -JM".