At least one man was struck down by lightning and killed while a woman was injured when her house collapsed, disaster management officials said.
The authorities set up 12 temporary shelters in and around the capital to accommodate the victims of the heaviest rains since June 1992.
The national assembly was flooded, forcing parliamentary Speaker Chamal Rajapakse to take a boat to inspect building, located on an island in a man-made lake, which is usually reached by a causeway.
MPs were later ferried over in military amphibious vehicles for a five-minute session, held in darkness, during which they passed six pieces of legislation under bipartisan agreement.
The red-carpeted main chamber itself was dry, but the assembly's lower floor was under more than a metre (three feet) of water, like other areas of the capital where thousands of homes were inundated.
Disaster management officials said between 250,000 and 300,000 people had been driven from their homes by the floodwaters.
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