An MRI was scheduled for later Monday to determine the extent of the injury, said Ole Miss coach Houston Nutt, who added that he expects to have a clearer picture of Shackelford's status today.
"We hope it's not too serious, but you never know," Nutt said.
Shackelford, a junior from Decatur, Ala., is penciled in as a starter at weak side linebacker and is considered one of the emotional leaders of the defense.
The workout was abruptly closed to media after several reporters filed news of Shackelford's injury on Twitter.
The school's media relations staff had previously indicated that "live tweeting" from practice was acceptable as long as media did not "speculate" on the nature of injuries witnessed during practice.
The practice was closed because training staff members determined information they were seeing was "speculative," a media relations staff member said.
For the portion of practice that was open, junior college transfer Zack Stoudt was the first in the rotation of quarterbacks to go through drill work.
Running back Brandon Bolden, who turned an ankle in Saturday's scrimmage, did not practice, but running back Jeff Scott, who sustained a shoulder injury, did.
A handful of other players who had been injured before the scrimmage, most notably defensive ends Gerald Rivers and Wayne Dorsey and linebacker Joel Kight, again did not practice.
Nutt said a review of the video from Saturday's scrimmage showed improvement in a number of areas. He singled out the offensive line, running backs, quarterbacks and receivers.