Meteorology Department today warned of incessant rain and thundershowers throughout the country.
Military personnel have been deployed to evacuate people living on slopes or in flood-hit areas. The navy was also helping clear choked canals in Colombo to stop low-lying areas including the country's parliament from flooding.
Nearly 5,000 families living in low-lying areas which have already been flooded due to the rains had been moved to relief centres, Disaster management centre spokesman Pradeep Kodippili said, adding that thousands of others have also left their homes to safety.
The rains have been lashing the country for the last two days, felling trees, damaging power cables and blocking roads and connectivity.
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"Three people are reported missing in Dehiowita area," Disaster Management Centre spokesman Pradeep Kodippily said.
Relief operations are well underway even the military had been deployed in the hill country areas to provide relief, he said, adding that the men went missing from the country's southwestern district of Kegalle.
Rains lashed the country throughout yesterday, flooding most of the roads in Colombo. Besides, several roads have been cut off due to floods with the Sri Lanka Red Cross saying its employees have been placed on alert to assist anyone who may be affected by the bad weather.
Katunayake, just outside Colombo, had recorded the highest rain fall, over 260 millimeters between 08:30 hours (local time) yesterday to 05:30 hours today, Meteorology Department said.
"The low pressure area is moving away from Sri Lanka so the rainy conditions over the island will be reduced to some extent, but strong wind conditions will continue for a few more days," Malinda Millagoda, a meteorologist said.
Yesterday, three international flights were diverted to Kochi in India due to bad weather conditions prevailing in Sri Lanka, Airport officials said.