Prior's agent John Boggs confirmed Friday that the right-hander has a tear in the capsule of his right shoulder, the shoulder he had surgery on in April 2007.
Prior had an examination and an MRI exam on his shoulder on Wednesday at the office of Dr. James Andrews in Birmingham, Ala.
Andrews is the doctor who performed the original surgery. The result was a torn capsule, which will keep Prior, 27, from throwing for at least two weeks.
"It's a setback, but in terms of how big of a setback, we won't know until you know how [Prior] is feeling," Boggs said. "We just hope it's not a major setback.
"Mark is looking at it in a positive way. He will just lay low for a few weeks and let the shoulder settle down."
Prior experienced discomfort in his shoulder while preparing for a bullpen session while at the Padres Spring Training facility in Arizona.
The Padres had initially hoped that Prior -- who signed a one-year deal worth $1 million on Dec. 26 -- would be ready to pitch in the Major Leagues by June 1.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.