McPhee, 28, will miss six to eight weeks after scans on Monday confirmed he had torn the posterior cruciate ligament in his left knee.
First-year midfielder Viv Michie, who appeared close to making his AFL debut, has suffered a stress fracture in his right foot and will have his leg in a cast for six to eight weeks.
Fremantle's injury list is the longest in the AFL with 14 players currently listed, including important midfielders Michael Barlow (leg) and Anthony Morabito (knee) and rebounding defenders Roger Hayden (foot) and Nick Suban (leg).
All four are at least a month away from returning, with Morabito sidelined for the season after undergoing a full reconstruction of his left knee last December.
Michie, Fremantle's second round selection (No.44 overall) in the 2010 NAB AFL Draft, has played seven senior games for WAFL side Peel Thunder, averaging 16 possessions in a high half-forward role.
The 19-year-old has impressed with his clean ball-use and shaped as a potential inclusion in coming weeks as Fremantle looks for a boost in its midfield.
Coach Mark Harvey said after Sunday's Western Derby loss to West Coast that he was being served well by too few, with the Eagles winning the clearances 41-35 against his side.
The coach refused to blame injuries, but said his team lacked class after its first Derby loss in four years.
Nathan Schmook covers Fremantle news for afl.com.au. Follow him on Twitter: @AFL_NSchmook
