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.
The storm with winds exceeding 110 kilometres per hour (70 miles per hour) reached the western mainland Friday.
Other boats in the area were approaching the migrant vessels to offer assistance, she added later.
No injuries were reported. The Civil Protection Authority said the western islands of Zakynthos, Kefalonia, and Ithaki had reported damage and outages and road closures from downed trees hitting power lines.
Greece's national meteorological service has issued a red alert and weather conditions are expected to continue for another day.
Aviation was disrupted with two Ryanair flights unable to land on the island of Cephalonia.
Local ferry services were also shut dow n.
Rare Mediterranean storm batters Greece's Ionian islands - SWI swissinfo.ch
As a precaution, migration officials said 778 asylum seekers, from three camps near Athens, would be relocated to a conference hall.
The 778 migrants from the camps of Elaionas, Malakasa and Schisto would be moved to a conference hall in Athens.
A further 28 minors from a fourth camp would be temporarily taken to a hotel.
"We're dealing with a total catastrophe", Nikolaos Gousios, a resident at Farsala, told state TV. A strong natural disaster also shook the island of Crete with a magnitude of 5.4.
Another boat sank at the harbour of Zakynthos but its Belgian occupants were unhurt, Kratsa said.
© Provided by Associated Press Seawater from crashing waves cover a road at the port of Argostoli, on the Ionian island of Kefalonia, western Greece, Friday, Sept. 18, 2020.
It was not immediately clear if he was among the two people reported missing. A year earlier, flash floods left 25 people dead and hundreds homeless in western Athens.
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