Morabito, who had been closing in on an AFL return, has flown to Melbourne to see a specialist.
"It'll definitely be the season, no doubt about that," Lyon told 6PR.
"It definitely doesn't look great but we've sent him to Melbourne to fully investigate it.”
Lyon said Freo would now wait on scan results and hoped it wouldn’t be another worst-case scenario for the 20-year-old.
"He's a special young player and he's had a rough run,” he said.
“When we get the specialist results we'll keep everyone informed.
"We really feel for Anthony and his family and Freo Dockers supporters who want to see him running around."
Morabito was recruited with pick No.4 in the 2009 NAB AFL Draft and had a solid debut season in 2010 before his injury.
