The Friends star, 53, has penned a memoir entitled Friends, Lovers And The Big Terrible Thing, in which he opens up about his widely-publicised substance abuse struggles.
Some excerpts have been shared ahead of the book's release and, according to reports, they include sections where Perry makes comments about Reeves.
He apparently seemed to have a pop at the actor in one part where he was discussing his late friend River Phoenix, writing: "River was a beautiful man, inside and out - too beautiful for this world, it turned out. It always seems to be the really talented guys who go down. Why is it that the original thinkers like River Phoenix and Heath Ledger die, but Keanu Reeves still walks among us?"
The star - who found fame as Chandler Bing in the hit US show - mentioned The Matrix star Reeves again when talking about comedian and actor Chris Farley.
Farley passed away in 1997 after an overdose.
Writing about the moment that he heard of the star's death, Perry wrote: "I punched a hole through Jennifer Aniston’s dressing room wall when I found out.
"Keanu Reeves walks among us.”
The comments sparked a backlash online and Perry has now told People in a statement that he was sorry and that he had chosen the name randomly.
"I'm actually a big fan of Keanu," said the actor.
"I just chose a random name, my mistake. I apologise. I should have used my own name instead."
Phoenix died in 1993 after a drug overdose, aged 23. Ledger died in 2008 at 28 as a result of an accidental overdose of medications.
Watch: Matthew Perry's heart stopped beating for five minutes