Barton is currently enjoying his loan spell at Marseille, but was quick to criticise his former team-mates following the Hoop's relegation on Sunday afternoon, describing some members of the squad as "maggots" and "w******" shortly after the team's 0-0 draw at Reading.
The 30-year-old - who was banned for 12 matches and fined £75,000 by the Football Association for his behaviour in the defeat on the final day of last season at Manchester City - revealed it would be tough to leave the French club.
However, Fernandes insists unless a transfer fee can be agreed, then Barton, signed from Newcastle on a free in August 2011, would be expected back at pre-season training.
"Marseille have got to put an offer in. Joey is under contract and Joey would be a very useful player for Queens Park Rangers," Fernandes said on QPR Player.
"He helped Newcastle out (of the Championship). Some would say we lacked his fighting spirit in the midfield.
"But if Joey and Marseille want (the transfer), then we will talk.
"However, he is a QPR player, and is contracted to QPR.
"That has to be a financial deal which would have to be worked out if he wants to go to Marseille, but as far as I am concerned he is a QPR player and in the summer will come back."
Harry Redknapp is set to remain in charge next season, despite failing to guide the club to safety after taking over from Mark Hughes last November.
The former Tottenham manager brought in the likes of striker Loic Remy and defender Christopher Samba on big-money transfers during the January window.
While both players are probably unlikely to be part of the Hoops' fight to regain their top-flight status, Fernandes remains optimistic the west London club will have a squad capable of mounting a sustained promotion challenge.
"We have been through it. There are many players we want to keep, some players we think don't want to stay and some players who are going to move on, but it is not insurmountable," the Malaysian businessman said.
"I am a positive person. People would say I am not realistic, but if you go through player by player, we will sort them out.
"You are not going to sort out everyone, there will be some...but I think every football club in England has players that they would rather not be there, but that is a function of the game.
"I don't think we are going to be in a bad position from that, we will come out okay."
Fernandes added: "We had a very good discussion. Harry has been very pragmatic, as have the shareholders.
"There are some players we really want to keep and we will do our best to keep them, and I think we will.
"Everything else is really Harry's call and the players'."
Hughes just managed to keep QPR up last season, and the club then moved to bankroll the purchase of men such as Brazil goalkeeper Julio Cesar, Jose Bosingwa, and Park Ji-sung last summer - all on big pay packets.
Fernandes accepts mistakes were made in the pursuit of sustained success, but insists a plan for long-term stability is now in place.
"We are in a position now we can trade, which we were never able to do because we were just buying, buying and buying," he said.
"We inherited a club which was in pretty poor shape, no training ground, a stadium which is clearly too small and a squad which really was not up to the Premier League.
"Much can be said about the buying process, but no-one can say we should have kept the squad as is.
"You could question some of the buys, but at the time you have to go with what the management says is good.
"I don't want to say it was anarchy and that just anyone came (here).
"We did not spend a lot in terms of transfer fees, which everyone fails to look at, apart from in the last transfer window when we brought Remy and Samba.
"There is a wage we are comfortable with now, how long we sign a player for and the wages we are looking at, that we have cleared up over the last few months."