According to an extract taken from Perry's book Friends, Lovers And The Big Terrible Thing, the actor appeared to take aim at Keanu Reeves.
"Why is it that original thinkers like River Phoenix and Heath Ledger die, but Keanu Reeves still walks among us?", Perry writes on page 6 of the book, which arrives on November 11.
In the book, Perry discuses the pair's mutual friend River Phoenix, who died from a drug overdose in 1993. He was 23 years old.
On River, Perry wrote, "River was a beautiful man inside and out and too beautiful for this world, it turned out".
He added, "It always seems to be the really talented guys who go down".
Another friend of Perry's was Saturday Night Live star Chris Farley, who also died from a drug overdose aged 33 in the same year as River Phoeinix.
"I punched a hole through Jennifer Aniston’s dressing room when I found out", Perry wrote when he heard about Farley's death, before adding "Keanu Reeves walks among us".
These comments have since drawn criticism, which prompted Perry to issue an apology.
"I’m actually a big fan of Keanu", Perry insisted. "I just chose a random name, my mistake. I apologise. I should have used my own name instead".
Elsewhere, Mathew Perry who played Chandler Bing in the popular 90s sitcom Friends, revealed that he was given a 2% chance of survival due to opiod addiction, which saw him in a coma for 2 weeks in 2018.