Sir Alex Ferguson has warned Wayne Rooney he will not walk straight back into the Manchester United team when he returns from injury because of the new challenge posed by Javier Hernández.

The Mexican has taken advantage of Rooney's absence to score three times in his past two games and Ferguson faces a dilemma whether to continue with the summer signing alongside Dimitar Berbatov or retain his faith in Rooney – who could be out for longer than first feared – despite the England international having been in the worst form of his professional life since the late stages of last season.

Berbatov has seven goals this season and Hernández, signed from Chivas de Guadalajara for £9m, has six, despite starting only five games. Rooney, in contrast, has managed one goal for United in the past seven months, a penalty against West Ham on 28 August, and his slide means he cannot be guaranteed a return to the side when he has overcome an ankle problem that could keep him out of at least three more games, including the derby at Manchester City on 10 November.

"His [Hernández's] performances have dictated that," Ferguson said. "We had a feeling he would break through and, therefore, it gives you a [selection] problem, but the right kind of problem. It will be difficult [leaving Hernández out]. I'm not even suggesting he will be left out. He's keeping his place in the team because he deserves to keep his place in the team."

United, trailing Chelsea by five points, face Tottenham Hotspur at Old Trafford tomorrow and Ferguson spoke of the need of "kicking on" now that the club have settled Rooney's contract. Rooney is still to issue the apology to fans that was promised but Ferguson is eager to draw a line under the matter.

"It's all over, it's all left in the past," he said. "He's signed a five-year contract, we're happy and we kick on. There have been plenty of difficult issues at this club over the years. You could say this was a big one but only in the sense it was a top player. Plenty of players come to a situation with their contracts. The difference is that they are normally done very quietly and unnoticed.

"But every club has these problems, once the players get to that two-year line when you have to start thinking about how to deal with it. All these issues are there for everyone these days. It's just much more difficult than it was even three years ago."

When Rooney will next be seen on the pitch remains unclear, the player having been injured in a training-ground tackle by Paul Scholes at the height of his dispute with the club. The initial diagnosis was that he would be out for three weeks, but the striker has been allowed to go on holiday with his wife, Coleen, to Dubai this week rather than having treatment.

"I think it will be a bit longer," Ferguson said. "He's away at the moment so there's no recovery. He's having a rest. He did his remedial work before he went. Thereafter rest is what he needs and we're quite happy with that."

At times last season the absence of Rooney would have been a devastating setback for United but Hernández's form has made it seem no longer quite so significant. "There is plenty of evidence the boy has got something," Ferguson said. "He's enjoying it here, his family are with him, he speaks the language, he's got desire, he trains very well, he's receptive to coaching, he looks after himself, he has good pedigree. His winning goal [against Wolverhampton Wanderers] on Tuesday demonstrated he's a very good finisher. Everything is in his favour."

Edwin van der Sar, 40 today, is set to become the first postwar player of that age to play for United but Ferguson will be missing two of his more experienced players, with Ryan Giggs due to resume training after a hamstring injury on Monday, and a similar problem expected to keep Michael Owen out for up to five weeks.

Ferguson reported more bad news when asked whether Owen Hargreaves was improving. "I can't see it, no. He was making very good progress but he seems to have stalled a bit and he's back with the physios now."