The midfielder was suspended for Sunday's 1-0 defeat against his former club Newcastle but some newspapers have suggested the new Hoops boss is planning to sell him.
Hughes, who also declined to elaborate on reports that QPR are closing in on January swoops for Brazilian duo Alex and Henrique, said: "I saw that as well and I think it's one of those maybe mischief-making Sunday-morning-prior-to-an-early-kick-off lead stories.
"From my point of view, there's certainly no suggestion that we are thinking in those terms.
"He is captain of the club, I have re-iterated that this week. Joey is a quality player and we are looking to bring quality in, not to get those type of players out of the building.
"It's fair to say we are in the market for good players if they become available and if they are attainable.
"We would like to think the players we are able to bring in would be the right quality, and I am sure they would be."
Meanwhile Hughes has said there is absolutely no chance of the club signing Carlos Tevez in January.
The pair worked together at Manchester City, before Hughes was sacked in the December of 2009, and there have been reports of a possible reunion at Loftus Road.
But Hughes told Sky Sports: "Not in this window, absolutely not."
Regarding the possibility of adding other new faces to his squad this month, he added: "If there's quality available and attainable then we'll pursue that but they have to be the right players and they have to be the players who can come in and make a major impact because otherwise there's no point bringing them."
Asked about Blackburn defender Christopher Samba, Hughes said: "It's common knowledge we've put in a bid for Chris Samba. We have a number of players we would like to bring to the club. We'll have to wait and see."
Leon Best's goal just before half-time settled the game in Newcastle's favour at St James' Park as Hughes made a losing start to his reign.
But the former Fulham and Manchester City boss took some positives from his side's performance and felt they deserved to get something out of the game.
He said of his players: "I was pleased with their application, they gave me everything they had, obviously we've been done with a little bit of individual skill in our own box.
"In terms of our play I think we created a number of reasonable chances and on another day those will go in for us. It would have been ideal obviously if we could have got something out of the game because overall I felt we deserved something.
"It's a hard place to come, we understand that, it was never going to be easy so that's why I'm encouraged by what I saw today."
He added: "We haven't had that much opportunity to work on our attacking play, it was more this week about making sure our shape was good and everybody knew what was expected of them and I think you could see that in our play.
"We were nice and solid, and everyone was working in relation to one another and that augurs well for the future and I think the longer we have the opportunity to work with the guys and given their application today, they'll only improve."