Air Malta has denied a report that a London-bound flight carrying Prime Minister Joseph Muscat was refused overflight by Swiss air traffic control. 

In a statement, the airline said the "slight delay" in the flight KM100 to London Heathrow on Thursday morning was caused by a "procedural error when submitting the flight plan". 

Due to this error, Air Malta said, the flight was held in Italy by air traffic control before entering French airspace. 

"The flight in question was not planned to enter Swiss airspace and the delay was only to allow the airline to update the flight plan with the French Air Traffic Authorities," it said. 

Air Malta made no mention of the Prime Minister's presence or otherwise aboard the flight. 

A report on manueldelia.com claimed that when control of the flight was handed over from Italian to Swiss air traffic controllers, the Swiss informed the plane of their decision to refuse permission for the plane to fly over Switzerland.

Dr Muscat is currently on a private trip to London with his family, days after returning from a brief holiday in Dubai. 

In recent weeks he has also visited the Vatican and Bethlehem, the latter being the only official visit of his recent travels. 

The Prime Minister is due to step down on January 12 after the election of a new Labour Party leader.