David Moyes has concerns over Wayne Rooney's immediate and longer term future, with the Manchester United manager admitting he must wait and see if the striker will consider signing a contract extension in the summer should they fail to qualify for the Champions League.

In the short term, Rooney's groin injury means he will miss Sunday's FA Cup game against Swansea City at Old Trafford and it could also sideline him for Tuesday evening's Capital One Cup semi-final first leg at Sunderland.

The forward has also entered the final 18 months of a reputed £300,000-a-week deal with the uncertainty about his future compounded by his being reluctant, it is understood, to enter any discussions until after the World Cup.

United's 2-1 home defeat to Tottenham Hotspur on New Year's Day left the champions 11 points behind the leaders, Arsenal, and increased doubts about their ability to finish in the top four. The champions are five points off fourth-placed Liverpool. At 28, Rooney is conscious he has only one major move left so wants to weigh his options carefully.

The Liverpudlian is enjoying one of the finest campaigns of a United career that is approaching a decade. Last season he was dropped and played out of position by Sir Alex Ferguson but Rooney has been restored to the side's focal point due to Moyes's faith in him and Robin van Persie's continuing injury problems. All of this has strengthened Rooney's position with regard to his next move and the prospect of playing for a club not in the Champions League may not be palatable.

Asked how confident Moyes would be of Rooney signing fresh terms if United did not finish in the top four, the Scot said: "Well, we would have to wait and see what [would] happen if that situation arose."

Moyes, though, believes Rooney is happy at the club. "I thought if you looked at his performances you'd have to say he's certainly playing at his best."

After the loss to Tottenham Moyes admitted that Rooney was carrying the groin injury and that he may miss matches due to it. This will now occur and the forward was pictured leaving Manchester's Bridgewater hospital holding a DVD containing the results of a scan.

While Moyes did not confirm the length of time Rooney may be out he did say that the striker will miss Swansea's visit to Old Trafford. "He's got a groin injury and won't be available for the game," said the manager, though he added that there was a chance he would be fit for Sunderland.

Van Persie, who has a thigh problem, and Ashley Young, who hurt a shoulder against Spurs, are also unavailable for Swansea, along with Phil Jones, Rafael da Silva, Nani and Marouane Fellaini.

Young, who had a scan on Friday, suffered his injury when being challenged by Hugo Lloris. "I don't know how long it will keep him out but he won't be available on Sunday," Moyes said. "It looks as if it's bad bruising at the moment."

Moyes reiterated his belief that United should have been awarded a penalty for the incident and that the Spurs goalkeeper should have been sent off by the referee, Howard Webb. "I don't need to repeat myself again and I'm not going to continue talking about it. I make mistakes," Moyes said. "Refs can make mistakes, I have no problem with that. I will try to own up to mine and stick my hand up if I get it wrong. Sometimes it would be nice if referees did that too but if they don't it's not a big thing for me. It's their prerogative. It's up to them how they go about their business."

Moyes's priority in the January transfer window is a midfielder and he would not rule out signing a player cup-tied for the Champions League. "I think it is important, but it's not the biggest thing because obviously you've got other games to play, FA Cup ties, League Cup ties, Premier League games," he said. "But if they are available you would like them to be able to play in the Champions League as well."

Despite speculation that United could revive their interest in Chelsea's Juan Mata, Moyes refused to discuss the playmaker and it is understood that the club will not move for the Spaniard or Ross Barkley in January. "I would never talk about players at other clubs. That is my stock answer. I didn't do it in the summer and I certainly would do it now," he said.

The Scot added that he would consider taking United away for a warm weather break if possible. "We could do if we felt there is time. Sometimes it can help. If I see the right opportunity then I could look at it," Moyes said.

• This article was amended on 6 January 2014. An earlier version referred to Rooney leaving Manchester's Bridgewater hotel. That has been corrected to Bridgewater hospital.