Recent reports have suggested that the QPR board are growing frustrated with the former Fulham coach and could sack Hughes if the team fail to get a result against Reading next weekend.
Fernandes said on Twitter: "Mark has my backing and the shareholders. We need a little luck and no injuries. What's written in the press is all rubbish. I honestly believe we have one of the best managers in the Premier League.
"And we are in for the long term. Whatever happens. We love QPR. I'll be there at Reading so Rangers fans I'll be available to meet and chat. Trust me on this one. Keep the faith. Stability is the key."
The club sit at the bottom of the league table after taking just three points from nine games.