Sir Alex Ferguson has cast serious doubt over whether Rio Ferdinand will accept a recall for England in what could prove to be a major embarrassment for the Football Association and the national manager, Roy Hodgson.

The Manchester United manager expressed great surprise at Ferdinand's inclusion in the squad – especially as the defender had not first been sounded out by Hodgson – and raised concerns regarding his ability to maintain fitness for his club. If Ferdinand decides against returning to the squad – as is expected after Saturday's game with Reading – it would signal the end of the 34-year-old's international career, as Hodgson would be reluctant to select Ferdinand again in case the same scenario was repeated.

Ferdinand has not spoken publicly about his call-up, despite usually being a regular on Twitter. While it is understood he is keen to play international football once more he is conscious that his club career comes first. Ferdinand is aware that while the final decision is his, Ferguson's preference is that he should allow himself the best chance of staying fit for United. An announcement is expected after the game at Old Trafford.

Ferdinand won the last of his 81 caps in June 2011 playing against Switzerland. Since then he has solved the persistent back problems that had previously plagued him to become a regular for United again.

England meet San Marino on Friday and Montenegro the following Tuesday. Both World Cup qualifiers are away and, after some considerable travelling by the England squad, United play two games in three days, the league trip to Sunderland then the FA Cup quarter-final replay at Chelsea on Easter Monday.

Ferguson said: "The issue is not that [the amount of games], the issue is his whole preparation for football today. It involves treatment, it involves rest, it involves heavy days followed by some light days followed by some easy days. Our preparation for Rio in games has been fantastic. Our medical staff and fitness lads have done a great job with him. That's the issue. Because he hasn't been playing international football when the international breaks have come along we have detailed all the things he has to do: when he trains, when his treatments come along. Therefore it is a disruption to his normal preparation."

Of Ferdinand's selection, the manager said: "I am very surprised. Of course it is a concern because he knows the procedures we have to go through. I will have a chat with him and the doctor and see what we should do about it. What he is enjoying is how we plan for him playing matches over the last two years and that has allowed him to reach his best performance level for quite a few years. He has been absolutely magnificent for us."

Ferdinand's selection represented a climb down for Hodgson. Previously, the England manager stated that he had "moved on" from any debate regarding whether Ferdinand should be picked again. This followed John Terry being chosen for Euro 2012 as Ferdinand was controversially left out. Hodgson claimed this was for "football reasons", though as Terry was facing trial at the time for the alleged racial abuse of Ferdinand's brother, Anton, following the championships – Terry was found not guilty – it had been questioned whether the pair could share the same dressing room.

Given the controversy over leaving Ferdinand out of Euro 2012 and subsequent squads despite him being first choice for United Hodgson may have been expected to call him to discuss his decision before Thursday's squad announcement. Instead, he called only Ferguson. "Roy Hodgson phoned me to say he had called him up and I was quite surprised and I did say to him that I will talk to Rio," said Ferguson, before insisting it will be Ferdinand's decision alone. "It doesn't rest with me it rests with Rio."

Ferguson is unsure how Ferdinand feels regarding the manner in which Hodgson discarded him. "I need to speak to Rio about that," he said. "I don't know what his attitude will be. I have not had enough time to do that. He has to make sure he's going to be OK in terms of the number of games he plays. The way we've detailed his training programmes and given him the treatments he needs for the various complaints he has in terms of his back and groin and things like that. So far it's worked very well. We have to look at all these things before Rio decides."

Ferguson also dismissed as "absolute nonsense" the claim from Rafael Benítez that he refused to shake his hand before Chelsea's 2-2 draw in Sunday's FA Cup quarter-final at Old Trafford. "Why wouldn't I shake hands?" he said. "Have you ever seen me not shake hands with anyone? I never saw him. I was signing autographs at the front. There was that Indian lad who always wants to shake hands before a game. He says it brings me luck.

"I was signing autographs. I never saw him. Why he said that I have no idea. If he wanted to shake my hand he could have stood in front of me."

Ferguson confirmed that Phil Jones's ankle injury and Nani's hamstring problem makes them unavailable for Reading's visit in Saturday's early evening kick-off. Both are unlikely to be fit before the Cup replay with Chelsea.