A wave measuring almost five feet hit Ciutadella on the west coast of Menorca in the early hours of Monday morning.
Nearby beaches were also flooded by the meteotsunami, called a rissaga in Catalan Spanish.
These are large, tsunami-like waves are triggered by disturbances in air pressure caused by fast-moving weather events, like thunderstorms.
Meteotsunami have been recorded reaching heights of 6ft (1.8m) or more.
The freak weather phenomenon also affected holiday resorts in Majorca, with seawater flooding bars and terraces by the coast in Andratx and covering beachside roads.
Andrew Sibley, of the Met Office, said: 'In certain conditions thunderstorms can trigger a phenomenon known as a meteotsunami, particularly in areas where the depth of the sea is sufficient to amplify wave height through resonance.
'The updrafts and downdrafts within a thunderstorm can create small and short-lived pressure changes, leading to initially small sea waves.
'These waves can then be amplified dramatically by resonance between the speed of the thunderstorm system and the speed of the wave if they are in phase.
'The speed of the sea wave is related to the sea depth. Such waves can also be funneled by coastal bays, estuaries and inlets.
'Meteotsunamis have been observed globally, including around the coast of Britain, but some regions like the Mediterranean are more susceptible.'
Boat owners in the resort on Majorca's south west coast were filmed desperately trying to protect their boats, with the footage shared widely on social media.
The strong current broke the ropes of a historic sailing boat used by the Majorca Island Council, which had to be rescued by sailors and brought back to port as it drifted out to sea.
There were no reports of any injuries and the meteotsunami occurred when the beaches were largely empty before holidaymakers started to arrive for their daily dose of sun.
The Daily Mail
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