Malinga’s departure is the latest setback for the maverick bowler, having been dropped as skipper after the team’s recent disastrous Asia Cup showing in Bangladesh.
“Sri Lanka team management on tour have observed that Malinga, whose niggling injury has been flaring up, would be better off resting it, and have recommended he return to Colombo,” the board said in a statement.
Malinga, 32, was last week retained in the squad with the board saying a replacement would be named shortly.
The bowler presided over a dismal showing by Sri Lanka in the Asia Cup where they were beaten by little-fancied Bangladesh, and only just scraped past the United Arab Emirates.
While Sri Lanka won the last World Twenty20 in Bangladesh in 2014, the team has been badly weakened by the retirements of star batsmen Kumar Sangakkara and Mahela Jayawardene.
Malinga only played one match in the Asia Cup where he hinted that he was considering retirement.
The paceman has had a long history of injury problems and gave up Test cricket in 2010, saying he was unable to withstand the rigour of five-day matches.