John branded the late singer's snub from this year's class "a total disgrace".
He told E! Online: "I'm so sad. This woman was the queen of disco and so much more. Her records sound as good today as they ever did.
"That she has never been inducted into the Rock and Roll Hall of Fame is a total disgrace, especially when I see the second-rate talent that has been inducted."
He continued: "She is a great friend to me and to the Elton John AIDS Foundation and I will miss her greatly."
Summer, who died at the age of 63 yesterday (May 17), was denied a place in the Hall of Fame after Red Hot Chili Peppers, Donovan, Laura Nyro, Beastie Boys and Guns N' Roses were inducted last month.
Online tributes for the star poured in on the news of Summer's death, including from Quincy Jones, who described her voice as "the heartbeat and a soundtrack of a decade".
Photo gallery - Donna Summer's life in pictures:
Copyright: Rex Features Andre Csillag/Rex Features