Rooney has always been one of the first names down on Ferguson's team-sheet at Old Trafford, but he is currently sidelined with an ankle problem and Ferguson has hinted that the emergence of Javier Hernandez is threatened the England striker's position.
With Rooney recovering from his injury in Dubai, young Mexican forward Hernandez has seized his chance to such an extent that United's star striker may not walk straight back into the side.
Hernandez struck late winners at Stoke last weekend and in the League Cup victory over Wolves in midweek. And United manager Ferguson is impressed by his new signing's exploits.
"Of course it will be difficult - I'm not even suggesting he (Hernandez) will be left out," Ferguson said. "He's keeping his place in the team because he deserves to keep his place in the team.
"We had a feeling he would break through, we had a good feeling about that. Therefore it gives you a problem, but the right kind of problem.
"There is plenty of evidence the boy has got something. He's young and he wants to learn.
"He comes from a really good football pedigree, everything is in his favour.
"He's first in before 9am and he's last to leave. So you get your rewards for your efforts and at the moment that's been the case.
"Javier's enjoying it here, his family are with him, he speaks the language. It's all good for him at the moment."
Ferguson looks to have pulled another rabbit out of the hat with the seven million pounds capture of Hernandez from Mexican side Chivas.
His scouting system has already seen him pick out the likes of Cristiano Ronaldo, Nemanja Vidic and Peter Schmeichel down the years.
Ferguson said: "I get satisfaction from anyone that does well here. Your judgement is always on the line - it doesn't matter if you pay 2p (pence) or two million pounds. You just hope he's successful.
"Over the years we've had some fantastic buys at all varying money. Money has increased in the last decade to different levels.
"Twenty years ago we brought players like (Steve) Bruce and (Brian) McClair for 800,000 pounds. What would they cost now?"
It has been a turbulent time at Old Trafford of late. From dropping precious late points to the Rooney contract saga, it's not been plain sailing for Ferguson.
Now with Rooney's future being solved, the Scot wants the focus to switch back to his team as they bid to wrestle the title away from Chelsea, who sit five points clear of United at the top of the table.
Ferguson said: "It's all over, it's all in the past. Rooney's signed a five year contract. We're happy and we kick on.
"The future is exactly as it was a few weeks ago. No-one has left the club, we have the same squad of players, we have issues with injuries so we're no different to everyone else.
"There have been plenty of issues over the years. You could say it was a big one last week. But only in the sense it was a top player.
"Plenty of players come to a situation with their contracts that you have to deal with. The difference is that they are normally done very quickly and unnoticed.
"But it's our job now to kick on. We've got important issues and that is chasing Chelsea. That's our aim - to catch them up."
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