The centre put the official death toll at 27. The floods were triggered by week-long rains across northern, central and eastern Sri Lanka that forced more than a million local residents to flee their homes.
Some 3,000 soldiers have been deployed in the worst-affected regions, along with trucks and air force helicopters, as UN convoys have struggled to bring crucial supplies in by road.
A large number of those forced out of their homes had only recently been resettled after decades of ethnic conflict between Tamil Tiger rebels and government forces.
"Many families were just returning home after years of displacement," said Reza Hossaini, country representative for the UN children's agency, UNICEF.
"They were rebuilding their lives, children were returning to their communit