Nunez was in action for United's development squad against Wigan at Elland Road on Monday afternoon but lasted just 15 minutes before going to ground in some pain while running with the ball.
The Honduran left the field on a stretcher and the Championship club are assessing the extent of the injury.
However, Under-21s coach Neil Redfearn is preparing himself for bad news.
He told the club's official website: "It didn't look good and when a player goes down like that your initial reaction is that it could be a long-term. If that's the case it's a shame for him, but he will be assessed as to what the extent is before we find out."
Nunez was placed on the transfer list by manager Neil Warnock at the end of last season, but has featured as an over-age player in the development squad matches this term.