They said that a woman went missing after she ignored police and firefighters 'instructions not to drive in an area where a bridge spans a river.
The rare storm is described as a "medicane" - a combination of Mediterranean and hurricane, as it has similar features to hurricanes and typhoons.
The Greek coast guard received a distress call from the boat on an emergency number on Friday morning, but its vessels were unable to approach the boat amid gale-force winds.
Parts of central Greece were also struck by the storm, with homes evacuated and several motorists reported stuck in their cars on flooded roads.
The General Secretariat for Civil Protection has repeatedly issued warnings since Wednesday urging citizens to be especially careful until Sunday, as the extreme weather front was forecast to hit the Aegean Sea islands in the coming hours.
It then swept through central Greece, hitting mainly areas around the cities of Karditsa and Farsala.
Ryanair airlines flight FR6611 from the United Kingdom to Kefalonia could not land at the island's worldwide airport on Thursday because of gale-force winds, as the Medicane "Ianos" is expected to slam into western Greece.
Seawater from crashing waves cover a road at the port of Argostoli, on the Ionian island of Kefalonia, western Greece, Friday, Sept. 18, 2020.
Storm Ianos could end up being one of the strongest medicanes on record.
"Trees are falling everywhere", Ionian Islands governor Rodi Kratsa told ERT on Friday and the state news agency ANA said a Swiss sailing boat moored off Ithaki was shoved to sea by waves. So far, there have been no reports of injuries or deaths, but a significant amount of property damage can be seen even in the limited local footage. And in 2017, a medicane caused a flash flood that killed more than 20 people.