Hughes stepped down from his role at Craven Cottage this afternoon but has since come out and said the choice to leave was not determined 'by any outside party'.
"I hope the supporters and all those connected with the club [Fulham] will understand I wish to move on to further my experiences," he said.
"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 has been heavily backed to take the job at Villa after Gerard Houllier left because of health issues but these comments have now made things unclear.
Regardless, Hughes is no longer the manager of Fulham and thanked everyone involved for his one season at the club.
"I would like to thank the chairman, directors, players and fans of Fulham Football Club for their support over the last 12 months and wish them every success in the future," he added.
"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 next season and for their continued progress on and off the field."