The 28-year-old speedster, whose unusual 'slingshot' action makes it tricky to face, has been told to rest after completing his Indian Premier League duties with the Mumbai Indians.
Malinga, who took 22 wickets in IPL 5, complained regarding a sore back and knee problems after the IPL campaign.
Fraser expressed his disappointment over Malinga's absence, "Naturally, we are extremely disappointed that Lasith will not be playing for Middlesex CCC in this summer's t20," Fraser said.
"I totally understand Lasith's concerns - his workload has been and is high - but I am disappointed we are the side to be denied of his services.
"A lot of work goes in to securing these deals and getting 'No Objection Certificates' from the relevant governing bodies.
"But we are not the only county to suffer in this way and over the coming days we will do all we can to secure the services of another high quality international cricketer for our t20 campaign," added the former England pace bowler and cricket correspondent.