The districts of Hambantota and Ampara, two of the worst hit by the December 2004 tsunami, were under water, sadi National Disaster Management Centre director N. D. Hettiarachchi.
"The flood waters are receding, but the victims will have to be looked after for a few more days," he said, adding that authorities were already providing cooked food to the homeless.
He said the flooding in the south and east was compounded by the overflowing of several irrigation tanks after heavy rains.
Sri Lanka, where 31,000 people died in the tsunami, depends on monsoon rains for farming as well as power generation.
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However, the seasonal downpours frequently also cause loss of life and damage to property in low lying areas.
The two main monsoons in Sri Lanka are from May to September and December to February. Rains also lash different parts of the island between October and November and again between March and April.