The Disaster Management Centre in Colombo said 311,000 people had sought refuge in state-run relief shelters by Monday morning, while approximately 900,000 were living with friends and relatives.
Monsoon rains only last month in the same areas of the north, east and centre of Sri Lanka killed at least 43 people and drove more than a million people from their homes.
The latest floods have washed away further large swathes of farmland in key rice-growing regions.
The Meteorology Department has warned of more wet weather in the next 24 hours.
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