Flooding hit the eastern district of Ampara, a largely flat agricultural area with a coastline that was hammered by the 2004 tsunami and where infrastructure has long been neglected because of a protracted war between the state and Tamil Tigers, after heavy rains began on Monday.
Mass displacement of people following seasonal floods are common in Sri Lanka.
The meteorology department forecast continued rainfall in coming days, but said it would not be heavy.
Flooding and drought are cyclical in Sri Lanka, where a southern monsoon batters the island between May and September, and a northeastern monsoon runs from December to February.
In December, 20,000 people were displaced in Ampara as a depression over the Bay of Bengal compounded monsoon rains.
The same month, 175,000 people took refuge in welfare centres and temples in the eastern and central parts of the country following flash floods.