San Diego manager Bud Black said Thursday that Prior might have "to take a step back" after reporting the soreness following his side session in Peoria.
There hasn't been a determination from the medical staff of how much rest Prior will need or when he'll possibly throw again.
Prior, who has had two significant surgeries to his right shoulder since 2007, had not reached the point yet where he was throwing to live hitters.
Prior has no defined timetable for a return to pitching in games, either at the Minor or Major League level.
"He's trying to work through that point where he's not feeling any soreness," Black said. "The poor guy just can't seem to get over the hump. He is doing everything possible for him to come back. ... I hope it works out for him."
Prior, a San Diego native, signed a Minor League contract with the Padres in January even while he was rehabilitating his shoulder from surgery to repair an anterior torn capsule last June.
That was his second shoulder surgery in 13 months, as he had arthroscopic shoulder surgery in April 2007.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.