Flooding caused by a week of rain has left 11 people dead and three missing, the centre said. The death toll could be higher, the centre added, because it had yet to receive reports from some of the affected areas.
Floods and landslides in central Sri Lanka have damaged more than 12,000 houses. Schools in some of the affected areas have been closed with many of them being used as shelters for the displaced.
More than 320,000 of those displaced were being accommodated in camps set up by the government, but many others took shelter with friends and relatives or in temples and churches.
Many of the flood-hit areas had only started to recover from flooding four weeks ago, which left 43 people dead and more than 1.1 million displaced.