Ekanayake said that 25 camps have been set up for displaced people.
The meteorology department has forecast rainfall for the forthcoming days as the southwestern monsoon starts.
West and south hit
The rains hit western regions of the island, including the capital, Gampaha and Kaluthara, and southern areas of Galle, Mathara and the gem-mining region of Rathnapura.
The problems of flooding are often exacerbated in Sri Lanka due to the country's neglected infrastructure after years of civil war between the state and the separatist Tamil Tigers.
In January more than 30,000 people were displaced in the east of the Indian Ocean island by monsoon flooding.
Flash floods in the east and centre of the country caused about 175,000 people to be displaced.