"Ben Ali is not coming to Malta and the government has no indications he'll be coming to Malta," Foreign Affairs Minister Tonio Borg said.
"The plane made contact with the control tower asking for permission to enter Malta's air space. The plane is going north," a foreign minister spokesman told AFP.
Rumours sweeping the Internet suggested Ben Ali may be hoping to find exile in Malta or Italy.
The Italian foreign office said Ben Ali was "absolutely not" on his way to Rome, and the rumours were "unfounded".