The stand-up made the comments in a reply to an email asking fans to choose their Fosters 'Comedy God' from a list of all nominees for the if.comedy and Perrier awards at the Edinburgh festival over the last 30 years, Chortle reports.
Awards producer Nica Burns was quoted in the release as saying: "Some 30th anniversary interactive fun - comedy punters can crown their favourite act. Upset the professional judges! Right some wrongs!"
Lee's response reportedly read: "You need to pull the plug on this now. It is the most shameful, inane thing I have seen in all the years I have been doing the Fringe. You will ruin it for everyone. Have a heart, for God's sake.
"This will discredit comedy in Edinburgh and play into the hands of your critics, who are all much smarter than you... How dare you proceed with this farcical, selfish idea?"
It continued: "You should be ashamed, Nica Burns! It's not too late to try and change the way you will be remembered... Corporate Whores. Morons. Illiterates.
"The whole thing will blow up in your face. Then, perhaps, we will see an end to your nonsense. Your cynicism is breathtaking. Your Edinburgh Comedy God idea is banal. There are no comedy gods."
"I am very sorry the talented Stewart Lee is upset," Burns said. "He obviously doesn't like the idea and, in his own inimitable style, has expressed himself very strongly."
Burns was also said to be "absolutely stunned" by the use of the word "whore", though Lee issued a clarification stating: "I wasn't using the word in a sexual or sexist sense, but in the commonly understood metaphorical sense of 'corporate whore'."