Hughes must reportedly beat fellow strugglers Reading on Saturday if he is to avoid being dismissed from the bottom of the table side who are still seeking their first win of the season.
But writing on Monday on his Twitter account, Fernandes claimed the club's hierarchy are behind Welshman.
"Mark has my backing and the shareholders," Fernandes said.
"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.
"Trust me on this one. Keep the faith. Stability is the key."