All Premier League clubs have to submit a 25-man squad list at the beginning of September, which cannot be altered until January.
Barton will miss the first 12 matches of the new season as a punishment for his actions on the final day of the last campaign against Manchester City.
With that in mind, Hughes has suggested that the midfielder may not make the cut.
"Joey's a contracted player here and his situation isn't what we wanted to go through. It's difficult for him, difficult for us," Hughes told the London Evening Standard. "Joey likes an input and to have a voice and I haven't got a problem with that.
"He knows what he did was unacceptable. He's been brought to book and he's trying to turn it around.
"I've got to make a judgement on whether or not I can afford to put him in the 25."
Barton has recently been linked with loan moves to Blackpool and Fleetwood Town.