The veteran midfielder has battled shoulder setbacks throughout the last several seasons, with a recent procedure having the 30-year-old face further "complications" with his surgery having "plateaued".
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The two-time Brownlow medallist was limited to just the 15 appearances this season due to a dislocated shoulder, with Fyfe now set to miss his scheduled return to training in December.
“Nat’s recovery from his initial shoulder reconstruction surgery had plateaued and, as a result of that, we sent him in for a scan which indicated that there was a small crack in the bone block that forms the basis of these types of surgery," Fremantle football boss Peter Bell revealed on Tuesday.
“We all know how diligent Nat is and he was complying with his program very well, however these bone block fractures are known complications of this type of surgery. As a result, Nat has undergone a revision of the surgery.
“Whilst it is disappointing, we know that he will be incredibly diligent in his recovery and a return to training date will be advised in due course.”
Fyfe hasn't played more than 21 games in a season for the Dockers since the club's grand final finish in 2013, with the contested ball-winner a key asset for his side's hopeful return to premiership contention next year.
Fremantle's five-plus year players are set to return to training on December 6, with Fyfe now facing delays and looking at a return later into the club's pre-season schedule.