Cooley will have surgery Wednesday.
Asked if Cooley will play again this season, Shanahan said: "We'll listen to (doctors') opinions over the next few days, especially after the surgery, to make a decision for sure."
Meanwhile, left tackle Trent Williams is expected to miss at least a couple of weeks with a severely sprained right ankle.
The injuries could lead to different starters at four of the five offensive line positions.
"It's going to be a big challenge," said Jammal Brown, the right tackle who might move to left tackle.
Copyright 2011 by The Associated Press