The Potters gave Swansea short-shrift over the chances of the Welsh star making an emotional return home.
The 27-year-old carved out his name with the Swans before moving on to Liverpool.
But Hughes underlined that the Welsh club had been left in no doubt where they stood on flogging their £13m playmaker.
Hughes said: “Not for sale – we didn’t give them any encouragement on that one.
“My understanding is that they made an enquiry but we rebuffed it straight away.
“It wasn’t a bid, more a question of whether we would be willing to let him leave. You’d like to think that because of our answer, they would respect that.”
Hughes said that Stoke appeared to have hit a brick wall over attempts to get Manchester City’s Fabian Delph to the club.
He added: “We’ve been down the road with that one and come up against a roadblock.
The financial package to get the former England midfielder in has proved prohibitive.
Hughes added: “I’m not sure that’s viable. It has no bearing or affect our feelings on Joe’s position.”
