Hughes's future at Loftus Road has been under scrutiny in recent weeks as the team's failure to win any of their first nine matches of the season has left them bottom of the Premier League table.
"You can't blame Mark for the position we're in but we're a vastly more consistent team than we were," Fernandes told QPR's official website.
"I'm an old-fashioned guy that believes in stability and changing things is going to achieve nothing. Cream eventually rises to the top.
"I'm fully behind Mark, as are the shareholders. We haven't had luck but we have enough quality in the squad."
The R's have the chance to get their first league victory on the board on Sunday when they entertain fellow strugglers Reading.