The Spaniard reportedly had a buy-out clause in his contract at the Britannia Stadium.
There were fears he could be set for an exit in the January transfer window though, with the Mirror reporting he has a £10million buy-out clause in his current contract at the club.
However, it seems those reports were false, with Hughes today insisting that no such buy-out clause exists in his contract.
“There's a lot of speculation on Bojan,” he told reporters, reported by the club’s Twitter account.
“There's a lot of misinformation about and there is no clause in his contract.
“I take transfer speculation with a pinch of salt. I don't know where the stories come from and a lot come with no substance.”
The news will likely come as a boost to Stoke fans, who would have been fearful of losing one of their star men this month.
The former Barcelona man has formed a dangerous partnership with Marko Arnautovic and Xherdan Shaqiri this season, with the trio being key to their rise into the top ten.
Losing one of them in January would have been a big blow to their current hopes of finishing in a European spot this season, although it seems that is unlikely to happen after Hughes' most recent comments.