The dual Brownlow medallist will have to be administered intravenous antibiotics for up to three weeks to treat the infection.
Fyfe underwent season-ending reconstructive surgery in late July and had recently gone backwards in his recovery, meaning he needed another operation last week.
The Dockers have not yet put a time frame on the 30-year-old midfielder's return to training.
"Unfortunately, Nathan's tests have indicated a bacterial infection, and as a result, he will undergo intravenous antibiotics over the next two to three weeks," Dockers football boss Peter Bell said.
"He won't be able to do much physically in the period the antibiotics are being administered intravenously."
"Nathan is optimistic and understands in particular the importance of the next two to three weeks to allow the IV antibiotics optimal effectiveness.
"We will advise a return to training date in due course, once there is more clarity around Nat's recovery."
Fyfe is crucial to Fremantle's plans of returning to finals next season after a six-year absence.
The Dockers finished 11th last season, one win and percentage outside the top-eight.
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