Brady, who underwent surgery Oct. 6 after tearing the ACL and MCL ligaments in his left knee in the first quarter of the team's first game of the season, had subsequent operations on the knee after it became infected.
That infection resulted in a buildup of scar tissue, which may require surgery on the knee, the Web site reported, citing an anonymous NFL source.
The scar tissue also has affected Brady's ability to begin fully rehabilitating his leg, the report said, and the repaired ligaments remain loose. Another surgery also could be needed for that condition, the Web site reported.
The Boston Globe cited league sources and sources close to Brady that dismissed the report. According to the newspaper, the infection appears to have cleared and Brady's rehab is progressing as expected.
Backup quarterback Matt Cassel replaced Brady as the starter and helped lead the Patriots to an 11-win season, but New England fell short of the playoffs when Miami beat the Jets on Sunday to win the AFC East.