Steven Nzonzi is in talks with Sevilla after Stoke accepted a bid of £7million for the midfielder.
But Mark Hughes has now confirmed Nzonzi, who is in the final year of his current contract, is talking terms with the Spanish side.
"It's been well documented there's been interest from Sevilla," Hughes said. "We've got to a point where the club is comfortable with the deal Sevilla have come up with, so we've given Steven permission to speak with them.
"It's not concluded yet - as we know with these things, it can fall down at the last minute. We worked really hard to convince Steven his future lay here - it didn't seem to be enough."
Sky sources understand the proposed fee is £7m, which is double the initial price Stoke paid Blackburn for Nzonzi on transfer deadline day in September 2012.
The 26-year-old has since made more than 100 Premier League appearances for City, scoring six goals.
Stoke, meanwhile, are continuing to pursue a deal for Xherdan Shaqiri, the Switzerland midfielder who left Bayern Munich for Inter in January.
A fee of £12m has been agreed, Sky sources say,and City are waiting for the 23-year-old to decide on a move.
Hughes said: "Some happen quickly, some take a bit more time. The key word is patience - you can't give up on things until they've run their course."
Goalkeeper Asmir Begovic is no closer to leaving the Britannia, according to Hughes, who expects the player to join the pre-season tour of Singapore at the weekend.
He said: "There've been discussions, but we're in the same place we were a couple of days ago, He's due to fly out on Saturday."
Watch Stoke take on Everton in the Barclays Asia Trophy live on Sky Sports 1 HD next Wednesday from 10.55am.