After an emergency meeting, the civil protection ministry said wind gusts will reach 88 kilometres (54 miles) an hour, especially in the southern Aegean and Sea of Crete.
Ports near Athens have been shut to ferry traffic to all but the nearest islands, affecting travel for tens of thousands of tourists.
The Athens National Observatory in a statement warned there was a "very high potential for wind-driven forest fires", particularly in the east and south of the country.
The mayor of Athens on Thursday also shut down the National Garden after a tree fell in one of the capital's busiest high streets, narrowly missing shoppers.