The striker suffered the injury during training with the England U21 squad ahead of their 9-0 victory over San Marino.
The 20-year-old missed the whole of last season with a serious knee problem, and United manager David Moyes had agreed to loan him to Wigan to build up his match fitness.
But the move is now on hold pending the results of scans on his foot, although Wigan boss Owen Coyle remains confident that Keane will follow United team-mate Nick Powell to the Latics next week.
"It is fair to say we have a verbal agreement with Manchester United regarding Will," Coyle said.
"He was away with the Under-21s this week and took a slight knock, so I spoke to David Moyes.
"Given the lad had a very serious injury we would always be guided by them in terms of when they think it is the right time for him to come out on loan.
"This week would probably be too soon but if the Manchester United doctor is happy with it, there is a possibility we could have that sorted by next week."
Keane made his first-team debut for United in 2011 and is regarded as one of England's brightest prospects, but the knee injury he suffered in May 2012 has stalled his progress.
But Coyle hopes to help get his career back on tract as he attempts to guide Wigan back into the Premier League.
"This is a lad who is going to be a top player," said Coyle. "He knows where the goal is and plays beyond his years in terms of his knowledge of the game.
"He is a player I have admired for many years. It would be great to add someone of that quality to the squad.
"David Moyes will keep me up to speed with that and we will see how that one pans out in the next couple of days."