Morabito, who was snared with pick No.4 in the 2009 national draft, hasn't played an AFL match since undergoing a knee reconstruction in December 2010.
The full extent of Morabito's latest injury is not yet known, with the 20-year-old to visit a specialist later this week after undergoing an MRI scan.
Morabito's return from his 2010 knee injury was delayed by a series of soft tissue injuries.
The powerful wingman finally made his playing return for WAFL side Peel Thunder earlier this year, but was heavily concussed three weeks ago and missed the past two games.
Morabito's 2012 campaign was then thrown into further disarray when he suffered his latest knee setback at training.
"At this stage we are awaiting medical advice to determine the nature and extent of the injury and we will be in a position to provide an update after that time," Fremantle football operations manager Chris Bond said.
Morabito notched 23 games in his impressive debut season of 2010, but has suffered nothing but injury heartbreak since then.
In better news for the Dockers, classy midfielder Nat Fyfe is on track to return against Port Adelaide in a fortnight after making good progress following shoulder surgery.
And defenders Zac Dawson (knee) and Antoni Grover (buttocks) could be available for Sunday's clash with struggling Greater Western Sydney at Patersons Stadium.
Fremantle sit in 10th spot on the table with an 8-7 win-loss record, but remain just percentage adrift of eighth-placed St Kilda, who take on ladder leaders Sydney at the SCG on Sunday.