The met office has raised the danger level of its thunderstorm warning to orange, hours after it issued a yellow alert.
It said that heavy thunderstorms probably accompanied by hail will affect the area. Locally, the accumulated precipitation may exceed 70 ml in a six hour period.
The orange alert is in force from 4 pm today to 11 am on Wednesday.
Heavy rain and hail as well as strong winds overnight led to flooded streets and houses in Nicosia and Limassol. Trees were uprooted and drivers trapped in their cars.
The Interior Ministry has announced that officials were assessing the damage and crews were helping in the clean up.