Rooney, who will miss Wednesday's Champions League game against Bursaspor due to his much-discussed ankle injury, has personally informed Ferguson that he does not wish to continue his career at Old Trafford.
Rumours that the player wanted to move on have taken up the front and back pages of many national newspapers in England in recent days, with reports emerging that he was unwilling to extend his current contract.
Ahead of Wednesday's Champions League game, Ferguson neglected to take questions from journalists but spoke solely - and at length - about Rooney's situation in an extraordinarily candid press conference in which he revealed Rooney's agents told United on August 14 that he did not want to sign a new deal.
Explaining why he would not be taking questions from journalists, Ferguson began: "I know that there could be a million questions on this subject. I can't answer them. I can give an opinion but that creates a side issue that we don't really need to get into, but we would like to present the facts.
"[United chief executive] David Gill had a preliminary talk with his agent at the end of last season, which was to be continued after the World Cup. [Gill] says, 'I've got some bad news for you'. His agent had intimated he wouldn't sign a contract and he wanted away.
"It's was shock. We couldn't believe it because, in earlier discussions - as early as February or March I think - he intimated he wanted to stay, he wanted to sign a life contract. He was happy at the club - he was at the best club in the world.
"I must say it was terribly disappointing when I got the news because we couldn't quite understand it. I had a meeting with him and he said to me, in his own way, that he wanted to leave."
Ferguson also expressed his disappointment that the news was made public and that Rooney has chosen to turn his back on a club and manager that have given him the platform to become one of Europe's finest players.
In a separate interview with MUTV, Ferguson added: "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..
"What we're seeing now in the media is disappointing because we've done everything we can for Wayne Rooney, since the minute he's come to the club. We've always been there as a harbour for him. Any time he's been in trouble, the advice we've given him - I've even been prepared to give him financial advice, many times.
"But you do that for your players, not just Wayne Rooney. That's Manchester United. This is a club which bases all its history and its tradition on the loyalty and trust between managers and players and the club. That goes back to the days of Sir Matt [Busby]. That's what it's founded on. Wayne's been a beneficiary of this help, just as Ryan Giggs, Paul Scholes and all the players have been. That's what we're there for.
"There's been no falling out. That's why we need to clarify the situation now for our fans. Because what we saw on Saturday was unacceptable. When we were at 2-2 and the fans were chanting for Wayne Rooney, it put pressure on the players and it didn't do any good for the team. So we've got to clarify the situation and try to do it right."
Reports emerged of a disagreement between Ferguson and Rooney when the player - who had been ruled out for up to three weeks with an alleged injury - said he had not had a problem with his ankle all season.
"The area has created quite a lot of the mystery about it as far as we're concerned - and probably you yourself, although you'll know more than I do - has been his injury," Ferguson said. "First of all, I must tell you that I have not had an argument with Wayne Rooney at all at any time. He got an ankle injury in the Rangers game, and was seen clearly hobbling about before half-time. He actually confirmed it himself in the interview with Sky.
"I spoke to him before the Sunderland game and our planning, based on the fact he wasn't playing that well, was to leave him out of the Sunderland game, make sure his ankle was properly prepared for the next game. Ten-day rest, ten-day recovery, so he could play for England (against Montenegro).
"The hope was, playing for England at Wembley, he could recapture his form and we could kick on. His entrance to the mixed-zone at Wembley [when Rooney told journalists he had not been injured] has created that next stage, which we've had to deal with.
"I was disappointed because we know fine and well he was carrying an injury. We sent him for a scan on the ankle injury - nothing serious, but it needed treatment and he's had treatment.
"We've got to a stage now where ... I feel that we still have to keep the door open for him, simply because he's such a good player, and we've done nothing but help him since he's come to this club. That's another mystery for us.
"I don't know how many times we've helped him in terms of his private life and other matters, and he's not the only one who gets that kind of privilege because Manchester United's that kind of club. We do that with all players.
"It's part of your job here that you look after your players, and that creates a tremendous loyalty - it's always been a good foundation of our club.
"We're as bemused as anyone can be as we don't quite understand why he'd want to leave a club that no one can deny is one of the most successful in British football. We've won 40 major trophies, countless cup finals, got a fantastic history, a great stadium, great training arrangements.
"We don't understand it, so I can't answer any question about 'why is he doing it?'. We can speculate, we can offer opinions - it won't matter a dickie bird, simply because the player says he's adamant he wants to leave.
"We have to deal with the next part of that, which we'll do as best we can, in relation to this request. I can't do more than what we've done and said at the moment because, in my mind, we still have the door open and who knows?"
