Stanton went on the disabled list April 30 after getting hurt a night earlier.
Manager Mike Redmond said Thursday that Stanton could continue to play catch and hit, but will not be able to run. The news meant there was no timetable on Stanton's return.
"He came in a couple of days ago with sore knees, so we've had to back him off," Redmond said. "He just started lightly jogging and just now complaining about his knees being sore."
Redmond said that calling him disappointed with the Stanton news was "an understatement."
During Marlins batting practice minutes later, Stanton was seen running lightly on the warning track.
Redmond, through a team spokesman after batting practice, said Stanton apparently ran on his own to test the knees.
Stanton is hitting .227 with three home runs and nine RBIs in 20 games. He appeared to be coming around offensively right before being injured.