Cleese created the comedy troupe with the Life of Brian star, who lost his battle with cancer in 1989, but he now admits he never really understood his friend and found him tough to work with, especially when his well-documented heavy drinking became a real problem.
In a new U.S. TV documentary series, marking the 40th anniversary of Monty Python's Flying Circus, Cleese reveals, "He just didn't work properly... The simple stuff - getting the lines right, hitting his mark, he just was not an efficient creature... He was always late."
Chapman's former partner David Sherlock insists Cleese was "most uncomfortable" around the funnyman after he discovered Chapman was gay.
In the documentary, Month Python, Almost The Truth (The Lawyer's Cut), Sherlock says, "He discovered he'd been working all this time with someone he thought he knew, but now discovered he didn't know."
Cleese admits, "We were all surprised... We didn't mind that he was gay, but we were very, very surprised and I think Graham, sometimes, took the surprise for disapproval."
And Cleese wasn't the only member of the comedy troupe who struggled with Chapman.
Terry Gilliam says, "Graham was just a frustrating person. I never could make out who Graham was."
And Terry Jones adds, "Graham was a mystery... The only times I had lunch with him, we really hadn't got much to say to each other, really."
Michael Palin admits Chapman's drinking problem was a real issue. He recalls, "Sometimes he'd be quite funny and other times... he'd just irritate people for the sake of it."
John Cleese, Terry Gilliam, Eric Idle, Terry Jones, and Michael Palin have agreed to take part in a get together at the Ziegfeld Theater in New York City on 15 October (09), where the quintet will be honoured with a special British Academy of Film and Television Arts (BAFTA) award for their contribution to film and TV.
The reunion event will also feature the premiere of new six-hour Python documentary Monty Python: Almost the Truth (The Lawyer's Cut).
The film will be shown in its entirety on U.S. cable channel IFC on 18 October (09).
Original Python Graham Chapman died from cancer in 1989.