Prior experienced discomfort in his surgically repaired right shoulder during a throwing session on Saturday. He will be examined by team doctors on Sunday.
"I think you can call it a setback," San Diego manager Bud Black said, "but we'll know more [Sunday]."
Prior experienced the soreness while throwing a batting practice session Saturday at the Padres Spring Training facility in Peoria, Ariz., that was cut short.
Prior has spent most of his time since Spring Training in Arizona, with several stops in San Diego as he works his way back from the shoulder surgery he had in April 2007.
There has never been a timetable for Prior's return to the Major Leagues, though there was once speculation it would be around June 1. But there's no timetable set for when he'll make any Minor League rehabilitation assignments first.
This is the second time Prior has experienced soreness or stiffness in his shoulder as he didn't throw for eight days in late April.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.