Malinga, 30, has not played Test cricket since 2010 but is a key part of Sri Lanka's one-day and T20 sides, which tour Bangladesh in February ahead of March's Asia Cup and T20 World Cup.
He was targeted by Sri Lanka's chief selector Sanath Jayasuriya for his fitness, saying he had work to do to be fit for upcoming tours.
"You have to admit that Malinga has a serious fitness issue," he said.
"But if he shows serious intentions and is willing to work hard and improve himself ... 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."
Melbourne Stars chief executive Clint Cooper said the club was upset to be losing Malinga and would seek to have him back for the finals, which begin on February 4, or to find a new overseas-based player.
"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," he 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.
"Our first priority is to do everything we can to have Lasith released for the semi-final, however at the same time, we are exploring alternative options to fill the void with other overseas players," Cooper said.
The Sydney Thunder have also lost Ajantha Mendis to the national call-up, though the perennial strugglers are again not in finals contention.
Malinga's loss will hurt the Stars, who have already lost James Faulkner, Clint McKay, Glenn Maxwell and Matthew Wade to Australian duty.
Ahead of the semi-finals, the Stars finish by hosting the Hobart Hurricanes on Tuesday night and the Perth Scorchers on Monday January 27.
Only two heavy losses would threaten the Stars finishing in the top two of the league and the home semi-final that would come with it.
Meanwhile, Perth Scorchers international signing Yasir Arafat has been ruled out of the remainder of the Big Bash League through injury.
Arafat injured the thumb on his right hand – his bowling hand – in last Thursday’s win over the Adelaide Strikers when he dived to field a ball early in the innings. His thumb became caught in the turf, rupturing a key ligament.
The 31-year-old bowled out the game with the injury.
Arafat will this week undergo surgery, ruling him out for the remainder of the BBL.
BBL regulations state that Arafat will not be able to be replaced by another overseas player as the paceman was already a replacement for original international signing Dwayne Smith.