Freeney hurt his left foot against the San Diego Chargers on Sunday and team doctors initially thought the franchise's all-time sacks leader would be out for about a month.
But they then amended their diagnosis, saying the injury to the three-times Pro Bowler would require surgery.
The Colts, first in the AFC South, placed Freeney on injured reserve on Wednesday.
The 27-year-old should make a "full and complete recovery in time for the 2008 season," the Colts said in a statement.
Freeney, the number 11 overall selection in the 2002 draft, has 60 sacks in his career. He produced 3.5 this season while forcing a team-high four fumbles.
The Colts (7-2) will be looking for three-times Pro Bowler Simeon Rice to fill in for Freeney.
Rice, 33, was claimed off waivers this week after being released by Denver.
(Writing by Steve Ginsburg in Washington; Editing by Tony Jimenez)

