Two Ryanair flights to the Ionian island of Cephalonia were unable to land at the local airport and were rerouted to Athens.
The Mediterranean hurricane, or "medicane", was packing violent winds of over 100 kilometres (62 miles) per hour, according to the Greek civil protection agency.
A sailing boat moored off the island of Ithaki was carried away by waves but its two passengers managed to make it to shore, state news agency ANA said.
The civil protection agency has urged those in the storm's path to avoid non-essential travel.
In 2017, flash floods west of Athens left over 20 people dead in one of Greece's worst natural disasters.
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