Fermanagh boss Peter Canavan says skipper Ryan McCluskey received his injury in an innocuous challenge in training.
"Fate has dealt him a cruel blow. He's been a very good captain and an inspirational leader for us," said Canavan, who added that Barry Owens will be handed the captaincy for the game against Down on 3 June.
Following medical examinations in Derry on Tuesday, McCluskey is expected to be out of action for at least 10 weeks.