The former Rotherham United and Preston player, who only joined Boro in January, suffered the serious knee injury at home.
It prompted Warnock to bring in former Leeds United captain Lee Peltier, who also worked with the veteran manager at Cardiff on a one-year deal.
Fears were abound that Fisher had sustained a bad injury and Warnock has confirmed that the 27-year-old - who joined the club on a two-and-a-half year contract, is now likely to undergo an operation.
Warnock, speaking after the club's friendly at Bishop Auckland on Wednesday night said: “We’re not sure at the moment but it doesn’t look very good.
“I’ll know tomorrow (today) but it’s looking like an operation and you’re talking nine months.
"We’re not optimistic about that.
“From what he’s telling us, it was a complete accident the way that he did it. It was an accident with a mate falling on him. Slipping and falling on him and crashing onto his knee.
“It’s the back of his knee or something. I can’t tell you the details I’m sure physios might do that. We’ll have to wait and see on that.”
Alongside Peltier, Boro have cover on the right-hand side of defence in the shape of fit-again Anfernee Djiksteel and Djed Spence, who both featured on Wednesday.
Warnock has also confirmed that Argentine midfielder Martin Payero, 22, has completed a medical. Some financial details need to be ironed out yet with the player also part of hius country's squad for the forthcoming Olympic Games in Japan.