Malinga is also expected to miss Sri Lanka's upcoming tour of England, as well as the Caribbean Premier League because of the injury to his left knee.
Sri Lanka Cricket (SLC) medical staff will now assess Malinga's injury and decide whether he needs a surgery or not.
"Malinga will present himself before the SLC panel of expert doctors on Wednesday (April 20) and depending on the outcome of the said medical examinations, be required to face a match fitness grading, after which SLC will take the next appropriate steps," the Cricket Board (SLC) said in a release.
Despite the Board not giving him permission to play in the IPL, the speedster has reportedly joined the Mumbai Indians squad on Friday and also took part in team's training session.
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Mumbai Indians are yet to make a statement on Malinga's injury.
Malinga sustained the injury during West Indies' tour of Sri Lanka last November, and has battled to regain fitness since then.
Malinga and the new SLC hierarchy have been at a standoff since the Asia Cup T20 in February.
Although Malinga made it to Sri Lanka World T20 squad as a player, he once again opted out of the crucial tournament, citing fitness issues.
As a result, Sri Lanka were forced to play the tournament without their main bowler, which turned out to be one of the main reasons for the defending champions ouster from the World T20 in the first round itself.
The SLC selection committee chairman Aravinda de Silva had said that he doubted Malinga's fitness claims and also insisted that his fitness would be proved when he would take part in the ninth edition of the IPL.