Some 13 people have been injured while another 115,000 have been forced to flee flooded homes.
The weather department said rains subsided by Wednesday afternoon as tropical Cyclone Mahasen moved away.
It is now threatening to make landfall between Bangladesh and Myanmar, and hundreds of thousands there have been told to move to safer areas.
Sri Lanka depends on monsoon rains for irrigation and power generation, but the seasonal downpours frequently cause deaths along with damage to property. (AFP)