The former test captain became the first Sri Lankan to take the job on a full-time basis since Roy Dias in 1999 when he was appointed last September.
The departure of the 44-year-old follows recent home test series defeats by Pakistan and India.
"Sri Lanka Cricket thanks Atapattu for his efforts as head coach and batting coach ... and we wish him every success in all his future endeavours," the board said in a statement.
Atapattu, who played 90 tests and 268 one-dayers from 1990-2007, became batting coach in 2011 and was then made head coach Graham Ford's deputy in 2013.
Following the resignation of Englishman Paul Farbrace in April 2014, Atapattu was named interim head coach and his team went on to win a test series in England and a test and one-day series at home against Pakistan.
Sri Lanka host West Indies next month in an encounter featuring two tests, three one-day internationals and two Twenty20s.
(Writing by Sudipto Ganguly in Mumbai,; Editing by Tony Jimenez)
Share
