The 64-year-old Monty Python star is at a private London clinic awaiting surgery, but doctors are confident that he will make a full recovery due to an early detection, the Daily Mirror says.
His agent Jodi Shield said the dad of two was in 'great spirits' despite the operation.
'He is having a routine exploratory operation in the next few days. His surgeon is fairly confident - they think they've got it early enough,' she said.
Fellow Pythonist Carol Cleveland told the paper she was 'praying' her co-star would be ok.
Jones was informed of the cancer before last week's West End premiere of Eric Idle's Monty Python and the Holy Grail-inspired musical Spamalot, but still attended the photo call.
The actor, who recently filmed a series re-examining medieval history for BBC2, directed Python films the Life of Brian, The Meaning of Life, as well as the Holy Grail, appearing alongside comic partners in crime Michael Palin, Idle, Terry Gilliam, John Cleese and Graham Chapman.
Chapman himself was a victim to throat cancer in 1989 at the age of just 48.
Bowel cancer claims 16,000 lives every year but if detected early is entirely treatable.
This sucks :(