The Melbourne Stars marquee fast bowler has been ruled out of the next two matches, with Sri Lanka selectors worried Malinga is becoming too fat in Australia.
The 30-year-old has failed to recapture the same devastating form as last summer's BBL, when he claimed a competition-best 6-7 against the Perth Scorchers.
Nonetheless his departure will hurt the unbeaten Stars' depth, with just two games left before the BBL finals.
Sri Lanka are currently playing a Test series against Pakistan in the UAE. Malinga is retired from Test cricket but is available for their ODI tour of Bangladesh next month.
They also want him to slim down before the Twenty20 World Cup begins in March.
"You have to admit that Malinga has a serious fitness issue," Sri Lanka selector Sanath Jayasuriya said.
"But if he shows serious intentions and is willing work hard and improve himself and if he is ready to show commitment towards national duty, then we feel it is unfair to leave him out.
"He is obviously a world-class bowler. So, we want him to prove himself by coming back from the Big Bash and working with our coaches and trainers and get back to his full fitness in the next few days."
Stars chief executive Clint Cooper admitted Sri Lanka Cricket had the final say on when and where Malinga played.
"While we are extremely disappointed to be losing Lasith at the business end of the tournament we respect the right of all national bodies to recall their players," Cooper said.
"We will continue to work with Sri Lanka Cricket around a possible return by Lasith for the semi-finals however a decision will not be made until he is assessed in Sri Lanka."
Malinga is certainly more rotund compared to last summer, but Cooper praised Malinga for his work ethic while with the Stars.
"Lasith has worked tirelessly on his game since joining the Stars after Christmas," he said.
"His preparation has been nothing short of first class and we are sure that this tournament holds him in good stead for the year ahead.
"We hope to see him return in green in BBL03 because he has become a valued member of our team, but if not, we wish him all the best for the year ahead with Sri Lanka."
Under the BBL tournament rules, the Stars will be able to seek an overseas replacement player.