A yellow weather alert is to stay in place until 11am on Thursday and may be extended if necessary the Met Office said on Wednesday, as Kyrenia, in the north, experienced extensive flooding.
Reports on Wednesday evening spoke of extensive floods in Kyrenia, which trapped drivers and blocked the road to Nicosia.
Extensive damage was also recorded in Nicosia and other areas.
After thunderstorms hit Nicosia on Tuesday, the heavy rain moved on to the Famagusta region on Wednesday causing flooding.
“We had 32 calls from the Famagusta district so far from 6.20am until now, mainly about flooded buildings,” said fire services spokesman Andreas Kettis. “There have also been reports of towing vehicles to safe places, rescuing people from their vehicles on flooded roads and fallen trees.”
Five groups from the fire service were currently working on the problem, and members of the civil defence and police have joined them.
The main road leading to Protaras was closed for three hours in the morning due to mud and was reopened after it was cleaned at around 11am.
Part of a newly fixed road in Pernera collapsed, raising questions why new roads such as this one and the one in Aglandjia which had problems on Tuesday are not able to cope with the rain.
There was no lightning such as in Nicosia, only a lot of rain, meteorologist Cleanthis Nicolaides said, explaining that the weather front had gained strength when it moved over the mountains, hence the Nicosia weather, but it has now moved further to the east and south with less energy.
Because of heavy rainfall, there have been landslides in the Limassol area, and drivers are urged to be careful and drive at low speed on the roads from Gerasa to Kalo Chorio, Gerasa to Louvara and Saittas to Karvouna.
More thunderstorms, rain and hail are expected during the next few days. Temperatures which were forecast to reach a maximum of 20C on Wednesday will drop until the weekend.