The yellow warning was issued at four in the morning and expires at noon, when conditions will gradually start improving.
More than 35 millimeters of rain per hour are expected.
Local showers and isolated thunderstorms are forecast for much of the day, accompanied by hail. Snowfalls are expected on the highest reaches of the Troodos mountains.
Conditions will improve in the early afternoon.
Winds will be southwesterly to northwesterly, moderate force four in the morning, but in windward regions and over the mountains, strong to very strong force five to six.
In the afternoon, winds will turn westerly to northwesterly, moderate to strong, force four to five, but in windward regions and over the mountains, very strong force six.
Seas will be moderate in the morning and rough in windward regions, turning very rough in the afternoon in western and northern coastal regions.
Temperatures will rise to 15 degrees Celsius inland, 17 in coastal regions and 4 on the mountains.
Clear skies this evening, turning partly overcast at intervals and the possibility of isolated light showers and snowfalls over the mountains.
Seas will be moderate in the east, moderate to rough in the south but very rough in the rest of the coastal regions.
Temperatures will drop to 5 degrees Celsius inland, 7 over southern and eastern coastal regions, 10 in the rest of the coastal areas and minus two over the mountains, where frost will form.
Overcast skies might bring isolated light showers and light snowfalls tomorrow, with conditions gradually worsening, bringing strong local storms, part of the ‘Leandros’ weather system that hit Greece earlier this week.
The same conditions will persist through to Wednesday morning.
Temperatures will gradually drop much lower than the seasonal average.