He signed a new four-year deal last year. But media reports suggest he has been looking for a move - with West Ham the top suitor - since Stoke ended last season 13th in the league.
"Marko and his people have put in a transfer request but that happens on occasions. Any comings and goings are at our discretion and it's our decision ultimately," Hughes told Stoke's Sentinel newspaper.
"Players can express an opinion or a view in terms of where they see their future but at the end of the day contracted players are contracted to the club and ultimately we have the final say," he added.
Stoke finished ninth in the league for three consecutive years, before slipping last season.
"We've never put him up for sale, we've never said he's for sale. Maybe clubs see a good player at another club and I would imagine there would be some interest from maybe one club," Hughes said without naming the side.
"There's been a bid but bids have to be reasonable and that one wasn't," he added.
The 28-year-old played in the first half of Stoke's 1-0 win over Swedish side Neuchatel Xamax on Monday.
(Reporting by Aditi Prakash in Bengaluru; Editing by Andrew Heavens)
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