Incoming flights were diverted to Sicilian airports while outgoing flights were delayed as bad weather conditions hit Luqa airport on Sunday evening, making it unsafe for planes to land.
People waiting to pick up arriving passengers were told that the planes were diverted because of low visibility and strong winds.
Sources said that the desert sand coming in with the strong winds could destabilise the aircraft.
Three flights were diverted to Catania and another to Palermo, according to the MIA website.
A flight from Paris was diverted to Palermo while the ones from Naples, Berlin and another one from Paris were diverted to Catania.
In a statement, Air Malta said that due to very strong winds over the Maltese Islands flights KM377 Berlin to Malta and KM477 Paris Orly to Malta were diverted to Catania airport. "The flights will return to Malta when it is safe to do so," the airline said.
All four flights made it to Malta some four hours after the original arrival time.
Passengers on one of the flights reported heavy turbulence on the plane as it was approaching Malta, forcing a decision to land in Catania.
Several flights leaving from Malta have been delayed as a result of the weather conditions.