The 27-year-old Malinga made himself unavailable for Sri Lanka's three Tests against England next month, citing a knee injury.
With Malinga continuing to play in the IPL for Mumbai Indians, Duleep Mendi, the Sri Lanka chief selector conceded the situation was "awkward".
The fast bowler officially subsequently announced his retirement from Test cricket, but he confirmed yesterday he will still be available for limited-overs internationals.
"There were lots of reports in the media insinuating that I might be feigning an injury to play in the IPL," Malinga said. "This was very upsetting as I have always been totally committed to playing for Sri Lanka."
Malinga denied that Sri Lanka Cricket had ever asked him to stop playing in the IPL and return to his home country for a rehabilitation programme.
"I assured them that I remain totally committed to playing for Sri Lanka," he said.
Malinga said he first sustained damage to his knee while playing in a one-day series in Australia in 2008. He has only played two Tests since then, both against India last year.
He said his is a "career-threatening" injury that prevented him from playing one-day internationals (ODIs) for 16 months and that his surgeon had advised him his condition will deteriorate when fielding or bowling for prolonged periods, taking months to recover after a Test match.
Malinga played 30 Tests, taking 101 wickets at an average of 33.15 after making his debut in 2004.
He has a much better record in the shorter formats and he starred for Sri Lanka in the team's run to the final of the World Cup this month, where they lost to India.
Malinga has taken 127 wickets in 84 ODIs, at 26.38. In Twenty20 internationals, he has 35 victims in 29 matches.