Prior was scheduled to pitch off the mound Tuesday, but he never got there. The shoulder flared up during long tossing.
"It wasn't getting loose so we weren't going to try it," pitching coach Larry Rothschild said.
The right-hander will be examined by Dr. Lewis Yocum.
"He had some posterior cuff irritation that obviously we need to get evaluated," trainer Mark O'Neal said.
Meanwhile, first baseman Derrek Lee visited Yocum on Tuesday after he bruised his left shoulder diving to catch a foul ball during the United States' victory over Japan on Sunday at the World Baseball Classic.
With the Cubs taking Wednesday off and Prior heading home to San Diego, the organization asked him to see Yocum. O'Neal wasn't sure what tests Prior might undergo.
"Hopefully, it's just a little snag," general manager Jim Hendry said. "When he said he had discomfort, that was the first time he had said that all spring."
The latest news about Prior only adds to the angst surrounding the pitcher's health.
Injuries have limited him to one spring training appearance the previous two years, and he started the 2004 and 2005 seasons on the disabled list. After returning from elbow soreness last season, Prior went back to the DL after being hit in the elbow by a line drive and finished with an 11-6 record and 3.67 ERA.
"He's had a zero-complaint camp," Hendry said. "When he said he had a little snag today, there's no sense in coming out Thursday without him seeing somebody."
Prior is trying to get in shape after being slowed by a throat infection during the winter.
"He hadn't had anything to this point," manager Dusty Baker said. "We'll keep our fingers crossed."
Hendry said there were no problems after Prior pitched two simulated innings on Sunday, and he was scheduled to pitch four on Thursday. But Rothschild seemed more concerned.
"It seems like it's a little bit more than that," Rothschild said.
The Cubs have said they would like Prior to pitch in three spring training games.
"Right now, I don't want to look at that," Rothschild said. "I don't want a timetable on what we're dealing with until we know
what it is."
Baker said Prior was "a little distraught. He wants to pitch. He wants to pitch with nothing wrong."