He suggested that his finest player could be sidelined by injury long enough to miss both the Manchester derby and England's next match, then hinted that, even when earning more than £200,000 a week, Rooney could not be sure of walking back into the team once he has recovered.
Taking a break: Coleen and Wayne Rooney in Dubai
With the emergence of Javier Hernandez there is now serious competition among the strikers at Old Trafford and Rooney's more recent form certainly would not justify his selection ahead of a gifted young Mexican now scoring important goals for the club. Five in the last six games.
As Ferguson agreed, it would be 'difficult' to omit Hernandez from his starting lineup.
'And I'm not even suggesting he will be left out,' said the United manager. 'He's keeping his place in the team because he deserves to keep his place in the team.'
The reports on Hernandez are extremely positive. Not only has he impressed his new colleagues with his performances on the pitch but with his attitude off it. While it is said that some of the young players at Old Trafford have not yet fully grasped what it means to be a Manchester United player, Hernandez gets it. He is focused and professional.
A player very much of the same mindset as a Ryan Giggs or a Paul Scholes and someone who, in the short time he has been in Manchester, already looks physically stronger. A not-so-little pea who will be unleashed against Tottenham today.
'We're all pleased with him,' said Ferguson. 'Everyone around the club is excited because he's done really well. He's got desire and he trains very well, and he's very receptive to coaching. He looks after himself and he has a good pedigree.
'He's working hard on improving physically. He's first in, before 9am, and he's last to leave. You get the rewards for your efforts and at the moment that's been the case. He's enjoying it here, his family are with him, he speaks the language; good manners. He's doing all the right things.'
There is talent as well, of course.
'His winning goal on Tuesday demonstrated he's a very goodfinisher,' said Ferguson. 'There is plenty of evidence that the boy hasgot something and we had a feeling he would break through. It gives youa problem but it's the right kind of problem.
'You never know how things will go. The boy has come from Mexico,where it's obviously a different culture. But we're not surprisedbecause we identified him and did a lot of work before we signed him.He's young and he wants to learn. Everything is in his favour.'
Red hot: Hernandez scores winning goal against Wolves
Rooney might have bemoaned a lack of ambition in the transfer market in that PR own goal of a statement but at around £7million, Hernandez is looking like something of a steal.
'I get satisfaction from anyone who does well here,' said Ferguson. 'Your judgment is always on the line if you pay 2p or £2m. You just hope he's successful. Over the years we've had some fantastic buys. Money has increased in the last decade to different levels. Twenty years ago we bought (Steve) Bruce and (Brian) McClair for £800,000. What would they cost now?'
Rooney has cost a fortune: in that initial transfer fee and now in the pay rise when he signed a new fiveyear deal last week. It might be a good deal less than Manchester City were prepared to pay in January - a fee, Sportsmail understands, in excess of £50m and what would have been the highest salary in football history of more than £300,000 a week - but still an awful lot of money.
It is a measure of Ferguson's confidence in Hernandez that he is not therefore rushing Rooney back after another setback with his ankle in training.
Ferguson told Rooney to take a family holiday knowing it would delay his return, mainly because he will not be getting the treatment that he would at Carrington.
Rooney now looks a doubt for the derby with City on November 10 as well as the friendly between England and France a week later. Ferguson said he would be out 'a bit longer' than three weeks.
'Wayne's away at the moment so there's no recovery,' he said. 'He did his remedial work before he went. Rest is what he needs and we're quite happy with that.'
Meanwhile, Spurs boss Harry Redknapp is confident he has closed the gap on last season's runners-up enough to end a nightmare run of 20 league games without a win at Old Trafford.
'We're getting better, we're closing the gap and we'll keep improving,' said Redknapp. 'There's no reason why we can't keep pushing for a Champions League spot.'
Closing the gap: Harry Redknapp
While full of respect for his good friend Sir Alex, even Redknapp struggled to disagree with Rooney's assessment that United are not the force they once were.
'He (Ferguson) has had so many great players, and built so many great teams, but they can't go on forever,' said Redknapp. 'Ryan Giggs, Paul Scholes and Gary Neville - they have been unbelievable. It's very hard to keep producing teams like that with David Beckham, Roy Keane, Giggs, Scholes, Andy Cole, Teddy Sheringham and Ole Gunnar Solskjaer. They are still great, but they are not as good as they were when Ronaldo and Rooney were in the team.'
United have been linked to Gareth Bale and Tom Huddlestone, but Redknapp is adamant that the days of Ferguson cherrypicking White Hart Lane talent are long gone.
'The chairman doesn't want to sell players we don't want to sell any more, 'insisted Redknapp. 'We're looking to improve. We're talking about January and we're trying to find maybe one player that would make the difference.'
So for Ferguson, the priority has simply been ensuring that Rooney still saw his future at United.
'There have been plenty of issues over the years ,' said Ferguson. 'You could say it was a big one last week. But only in the sense that it was a top player. Normally these things are done very quietly. But Wayne has signed a five-year contract and now we kick on. We're chasing Chelsea. That's our aim now, to catch them.
'The area that has given us most concern has been throwing games away. Fulham, Everton, West Brom. That's six points given away. We've given the rest a six-point start so we have to catch up.'
Starting with Tottenham today, with Hernandez in attack.
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Explore more:People: Paul Scholes, Alex Ferguson, Andy Cole, David Beckham, Ryan Giggs, Harry Redknapp, Teddy Sheringham, Roy Keane, Wayne Rooney, Gareth Bale, Gary Neville, Tom Huddlestone Places: Manchester, France, United Kingdom, Mexico