The Liverpool striker had been of interest to Sunderland earlier in the transfer window, but his wage demands may now see him remain at Anfield after a £10 million fee was agreed
The Loftus Road outfit seemed destined to beat Sunderland to the striker's signature after agreeing a £10 million fee with Brendan Rodgers's side.
But Fernandes has claimed the player and his agent have not been realistic with their demands as the transfer deadline approaches.
"I’m not confident Borini will happen. With player and agent expectations, sometimes people aren't very realistic, and we’re not going to be silly with what we do," he told Sky Sports News.
"There’s always ways of doing things but I’m not confident."
Goal understands Tottenham midfielder Sandro is close to completing a move to the Rs while Niko Kranjcar has arrived at Loftus Road to complete a deal to bring him back to the Premier League.
And despite looking set to miss out on Borini, Fernandes did admit interest in bringing Jermain Defoe to the club.
Toronto FC have insisted the player is not for sale, though, but Fernandes has left the door open for a January move.
"There’s a will from both sides but its whether the Canadians are willing to release him now," he continued.
"They’re in the play-offs so they’ll have to make some decisions. If not now then maybe in January something will happen."