Richard Bucknall, his former agent and promoter, said the "formidable" comic died in hospital on Monday and would be remembered for his "superb wit".
Hughes was a team captain on Never Mind the Buzzcocks on BBC Two and had his own Channel 4 sitcom, Sean's Show.
Fellow comedians, including Al Murray, Katy Brand and Jason Manford, have been paying tribute to the performer, who was also a writer and actor. In 1990, Hughes - then 24 - became the youngest person to win the coveted Perrier Award - now known as the Edinburgh Comedy Award - at the Edinburgh Festival.
"I was told that I had won the Perrier award as I walked off stage after another sweaty performance," Hughes later wrote in The Guardian. "The judging panel rushed on to the stage to congratulate me.
"'Will it go to his head?'. I doubt it. If the panel had made it 10 minutes earlier, they would have seen two people walking out of my award-winning show."
Nica Burns, director of the awards, remembered him as "a huge talent" and "a very good writer" who had "instinctive timing from day one".