The Daily Mail says Ferguson believes Rooney has failed to get on top of the weight and fitness issues that have dogged him since the start of the season and is fed up with waiting for an improvement.
With Rooney, 27, entering the final two years of his contract this summer, Ferguson knows he has a decision to make about his future.
As it stands, the Scot will not rule out selling him at the end of the season if the club can attract a bid of more than £20million.
Sources in both camps say the relationship between the pair has been tense for some time and shows no signs of getting better. Senior players say privately that they can sense it at the training ground on a daily basis.