The worst affected area was the southwestern Kalutara district where 10 people were killed. A rainfall of 200 millimetres was recorded in the Neboda area of the district.
Most of the access roads in all parts of Kalutara district remained submerged in water.
"In the Kalutara district, 10 people have died while one person is missing. In the Colombo district, two deaths have been reported while another person had disappeared from the Gampaha district," said Pradeep Kodippily, the Deputy Director of the National Disaster Management Centre.
"Strong winds of 70-80 kmph are expected to sweep through the island from eastern direction," said a weather bureau official.
Fishermen have been warned of the adverse weather as heavy rains are expected to continue.