Hughes’ decision to activate a break clause in the two-year deal he signed with Fulham last summer will fuel speculation of a move to managerless Aston Villa.
According to a source close to the club, owner Mohamed Al Fayed believed Hughes was positioning himself for a move while negotiating and finalising the terms of a new deal with Fulham.
Al Fayed is said to have grown “increasingly annoyed” with Hughes and did not oppose his request to leave at the end of June, having served a month’s notice.
But Hughes, in announcing his decision to leave Craven Cottage after one season at the helm, insisted he had not been in talks with any other club.
“I hope the supporters and all those connected with the club will understand I wish to move on to further my experiences,” said Hughes.
“I would also like to take this opportunity to clarify that neither myself nor my representative have approached or have been approached by another club.
“This decision to leave Fulham has not been influenced by any outside party.”
Hughes, 47, is the bookmakers’ favourite to replace Gerard Houllier at Villa Park, although the Midlands club are believed to be interested in former Chelsea manager Carlo Ancelotti.
Villa are also keen to make an appointment this month. If they want Hughes, they may have to wait.
The Welshman’s notice at Craven Cottage expires on June 30, the same day Fulham are scheduled to play the first Europa League qualifying round.
Fulham have confirmed that, even if a new manager has not been appointed by the end of the month, Hughes will not take charge of that game.
Hughes’ decision leaves Fulham searching for a new manager for the second consecutive summer, after losing Roy Hodgson to Liverpool last year.
Leading candidates for the hot-seat could include former Tottenham manager Martin Jol, ex-England boss Steve McLaren or Martin O’Neill, Houllier’s predecessor at Villa.
Hughes did well in his season with Fulham, guiding the club to an eighth-placed finish in the Premier League and earning them a return to Europe via the Fair Play League.
He also built on a reputation initially forged at Blackburn and then Manchester City, where many felt he was unlucky to lose his job.
“I would like to thank the chairman, directors, players and fans of Fulham FC for their support over the last 12 months and wish them every success in the future,” said Hughes.
“I believe my management team and I have done a good job and the club has a strong foundation from which they can go forward.
“I have especially enjoyed our excellent relationship with the chairman and chief executive (Alastair Mackintosh). I sincerely wish Fulham a successful campaign in the Europa League and for their continued progress on and off the field.”