Thunderstorms and hail hit some areas of Nicosia on Wednesday afternoon when only scattered showers had been expected.
Videos on social media showed some roads in the Tseri area of Nicosia flooded by the rain.
The meteorological service added that the weather would be partly cloudy with light fog by the evening. Temperatures were expected to fall to 21C inland and on the coast, and 17C in the mountains.
On Thursday, the weather will be settled but partly cloudy in some areas.