The English international was left out of today's squad for the 2-1 win over Swansea City at Old Trafford, because Ferguson - who retires from management at the end of the season - said the striker "was not keen to play because he has asked for a transfer". The 27-year-old previously asked to leave the club before signing a five-year deal in 2010.
Rooney has often had to play second fiddle to Robin van Persie this season and has not scored for the club since the middle of March. He was not even among the substitutes at Old Trafford this afternoon.
"I don't think Wayne was keen to play, simply because he has asked for a transfer," Ferguson told Sky Sports. "I think he wants to think it through in his mind - I think that's a good idea. We're not going to let him go. I think maybe he is a bit frustrated. He has been taken off once or twice in the past couple of weeks."
His new manager David Moyes, who first gave Rooney his debut as a 16-year-old at Everton, will now have to tackle the fall-out of the current impasse between player and club.