The Dockers say they are expecting to know the results of scans on Morabito's left knee later on Wednesday.
Morabito limped from Fremantle Oval, visibly distraught, with a left knee injury after twisting awkwardly during a tackling contest.
The high draft pick has torn the ACL in his left knee twice during his short career.
Fremantle football boss Chris Bond said Morabito was tracking very well towards his return to AFL football in 2013 before going down on Wednesday morning.
"We can confirm he has injured his knee, he has gone straight away to get some scans done and we are expecting the results of those scans in no more than two hours," Bond said.
"It's obviously a concern with Anthony's history, (Dockers coach) Ross Lyon has gone with him as well as the medicos, to make sure we are there to help him and assist him as best we can.
"There is a great deal of anxiety there not knowing exactly what the case is, he's got some really good people around him."
Bond refused to confirm whether Morabito would undergo another a full traditional ACL knee surgery, should scans show the worst.
"We will get the results and we will work out an action plan from there," Bond explained.
"Our number one focus at the moment is Anthony, we're hoping for the best."