The team is awaiting on results from an MRI, but they fear it may conclude surgery is necessary.
Lee, the team's leading tackler and defensive signal caller, was reported to have sprained his toe midway through the third quarter in the Cowboys' 19-17 win over the Carolina Panthers in Week 7.
Lee had 131 tackles last season struggling through much of it with a dislocated wrist.
Dan Connor, a fifth-year veteran and college teammate of Lee's at Penn State, would replace him as the starting middle linebacker, and Bruce Carter would become the defense's signal caller. A third-round draft pick in 2008, Connor played his first four seasons with the Panthers.
The Cowboys are at home against the Giants in Week 8, then hit the road against Philadelphia and Atlanta in Weeks 9-10.