Fergie has held a meeting with Rooney and his agent, where the 24-year-old admitted he does not want to sign a new contract with the club.
“David (Gill, chief executive) telephoned me and said he was on his way over because he had some bad news,” Ferguson told MUTV.
“His agent said he wouldn’t sign his contract and wanted away.
“Dealing with the next step was always going to be decisive for us, how we dealt with the situation.
“I asked to have a meeting with the boy and he reiterated what his agent said, that he wanted to go.
“The one thing I said to him was ‘respect this club’, I don’t want any nonsense from you.
“I don’t know if he has done that. I have doubts on that, we are reading all these things about falling out with me and all that nonsense.
“It’s disappointing because we have done everything we possibly can to help Wayne Rooney ever since he came to the club.
“We have always been here as a harbour for him any time he has been in trouble, the advice we have given him, I was even prepared to give him financial advice.
“But it’s not just Wayne Rooney, we have done that for all the players.
“Wayne has been the beneficiary of that, just as Ryan Giggs, Paul Scholes has…so there has been no falling out.
“So there we are, we have got into a situation where we had to clarify this for our fans because what we saw on Saturday was unacceptable.
“When we got to 2-2 (against West Brom) and they were chanting Wayne Rooney, it’s a pressure on the players and didn’t do the team any good so we had to clarify the situation and put it right.”
Ferguson added: “It was a shock. I couldn’t believe it.
“In early discussions – in March I think – we had discussions with him, he intimated he wanted to stay, that he wanted a life contract with the club, that he was at the best club in the world. It was terribly disappointing to get the news.
“We couldn’t understand it.”
“There’s no offer on the table as they are not prepared to listen to an offer but there’s always an offer from Manchester United to negotiate with any player and that’s still there,” he added.
“I am disappointed, I can’t believe it. When you manage Manchester United there is always something you have to deal with and we have had to deal with these situations before. It’s not as easy as it was a few years ago.
“We are dealing with agents who are living in the pockets of players, it’s a different world and we have to deal with it.”