Military helicopters were deployed to send food for marooned people in the central and and southern regions, which were flooded by heavy monsoon rains that also caused mudslides.
"So far we have reports of at least 16 people who were killed due to floods and mudslides," the centre's spokesman G.
M. Gunawardena said.
He said a total of 61,281 people were driven out of their flooded homes.
Flooding in the south was compounded by irrigation reservoirs, which overflowed after the heavy rains.
Sri Lanka depends on monsoon rains for farming and power generation. However, the seasonal downpours also 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.