The Met Office has issued a yellow alert for Thursday warning of isolated heavy thunderstorms. It said the rain intensity may locally exceed 35 millimetres and may be accompanied with hail.
The yellow alert is in force from 6 am to 6 pm on Thursday.
In an explanatory note accompanying the yellow alert the Met Office said: Be aware that thunderstorms may occur. Take extra care in exposed areas, like mountains, forest and open terrain. Disruption to outdoor activities is possible.
The warning comes as storms continue to batter the island. These are expected to continue tomorrow and abate on Saturday but more unsettled weather is forecast for Sunday.
Limassol bore the brunt of the storms last night, with the fire service saying they had responded to 29 telephone calls for help. Strong winds felled trees and shattered shop windows, while the fire service was also called to pump water from flooded buildings.
The fire service also responded to a call to remove a fallen tree in Polis Chrysochous and one in Evrychou, he added.
In its early morning weather forecast, the Met Office said low pressure south of Cyprus is continuing to affect the area.
Thursday will be mainly cloudy with local rain and isolated storms which may be accompanied by hail and locally may be heavy. Winds will be medium to strong, and in storms up to 6 to 7 Beaufort.
Temperatures will be 21 C inland, around 23 C on the coasts and around 11 C in the mountains.
Tonight will remain mainly cloudy with rain and isolated thunderstorms. Thunderstorms may be accompanied by hail and locally the phenomena may be strong, it said. Temperatures will fall to 18 C inland, around 21 C on the coasts and 10 C in the mountains.
Friday will be partly cloudy and at intervals mainly cloudy with local rain and isolated thunderstorms with gradual improvement from the afternoon.
On Saturday there will be periods of sunshine and periods of increased cloud which at midday and in the afternoon may lead to isolated showers or thunderstorms mainly in the mountains, inland and in the southeast.
On Sunday the weather will initially be cloudy becoming later by intervals mainly cloudy and leading to local rain and isolated thunderstorms, mainly after midday.
Temperatures will edge up until Saturday to close to average for the time of year but drop to below average on Sunday.