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 the 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.
Irrigation Minister Nimal Siripala de Silva said the flooding was caused by the loss of marshes in Colombo which had previously acted as a sponge to soak up water during downpours.
Most of them have been drained for housing development.
“There is message in this disaster,” de Silva told reporters outside the flooded parliament. “We need to take more care of our environment and pay more attention to protecting our eco-systems.”
Overnight rains dumped 44.5 centimetres (17.5 inches) of rain on the city, the biggest deluge since June 1992, when 49.7 centimetres fell in a day.
“We are deploying troops to rescue people who have been marooned as well as to clear dozens of cars struck in flooded roads,” said Colonel Dampath Ratnayake who was coordinating relief at the Colombo Operations Command.
“The storm water system is unable to cope with the volume of water and we are also sending troops to help municipal workers clear some of the blocked drains,” he said.
Navy boats and airforce helicopters were deployed to help stranded residents and police said thousands of houses were under water. There were no immediate reports of casualties.
Telephones and Internet connections were also cut because of lightning damage to telecommunication towers, while the authorities shut most public schools and cancelled a national examination.
Many banks shut down their automatic teller machines as their computer networks were affected by the lightning. Most landline telephone connections were out, and fallen trees brought down power lines.
A three-day practice match between the West Indies cricket team and a select XI was called off as the venue for the game in Colombo’s fashionable Cinnamon Gardens area was knee-deep in water, officials said.
On the roads police deployed extra officers as traffic lights failed and some of the flooded thoroughfares were blocked with stalled vehicles.
“Heavy rains are due to intermonsoonal activity and we can expect more rain,” national weather chief G. D. Samarasinghe said.
Sri Lanka depends on monsoon rains for irrigation and power generation but the seasonal downpours frequently cause loss of life and damage to property in low-lying areas.
The island’s two main monsoon seasons run from May to September and December to February, with rains in between being the result of inter-monsoon activity.