Flores is expected to fly to Birmingham, Ala., to see Dr. James Andrews to check on the shoulder. There is no timetable as to when Flores will return to action.
"Let's let us evaluate what's going on with the films and let the doctor do [his job] before we talk about the seriousness of the issue," acting general manager Mike Rizzo said. "There has been a setback. You will be updated when we know more over the next few days.
"We got an MRI and we are going to evaluate it. We're going to get a second opinion for him on Monday."
Flores suffered the shoulder injury against the Diamondbacks on May 9. In the bottom of the seventh inning, the backstop was hit on the shoulder by a Chris Young foul tip. Flores was in pain for several minutes, but he remained in the game before being taken out in the bottom of the ninth inning.
Bill Ladson is a reporter for MLB.com. Michael Radano contributed to this report. This story was not subject to the approval of Major League Baseball or its clubs.