The actor was scheduled to perform at the event for a second year in a row, but changed his plans after he discovered that filming for the movie adaptation of Stephen King's The Dark Tower would clash.
Speaking from the set of the anticipated film, Idris told his followers on Facebook that he was heartbroken about having to cancel.
It is with a very heavy heart that I let you know that I can't make it this year," he said. "I had to cancel my gig at the very last minute."
"Last year I had a wicked time. A lot of you came out and heard me DJ for the first time, and I was so looking forward to coming back and doing it again."
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He added: “It’s not my fault. I tell you it’s my film schedule, it changed at the last minute and I had to cancel.”
Glastonbury 2016 will be broadcast live across the BBC from this Friday, with Hello singer Adele set to hit the stage on Saturday night.
Although the Avengers actor appeared to be the firm favourite when a former James Bond star backed him for the role.
Asked whether a black actor could play Bond the star, George Lazenby said: "Why not? It would be a good idea."
Last year, Tom ranked 12th in a Time magazine poll of contenders, behind Idris, Jude Law and Benedict Cumberbatch.
