Flores was scheduled to be activated from the disabled list Friday, but he suffered a setback while at Double-A Harrisburg.
Flores suffered the shoulder injury against the D-backs 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. The original diagnosis was a right shoulder contusion.
"It's a minimum of three months. It could possibly be for the rest of the season," acting general manager Mike Rizzo said. "It's a bad day for the organization. It's not a devastating injury. It's going to take time to heal. Once it heals, we should have him at 100 percent."
Flores, who was hitting .311 with four home runs and 15 RBIs, was in a sling and devastated after hearing the news.
"When you play baseball, you know anything can happen any day," Flores said. "That day has come to me. I'm on the DL now. It's going to be really tough. I like to be there with the guys, playing every day. I can't explain how I feel right now."
In other news, the Nationals activated outfielder Elijah Dukes from the 15-day disabled list Tuesday and placed right-hander Kip Wells on the 15-day DL, retroactive to Sunday, with a right adductor strain.
Dukes, who started in right field Tuesday against the Giants, missed 13 games with a left hamstring strain. In two games during his rehab assignment with Double-A Harrisburg, he went 2-for-8 with a walk.
Wells has an 0-2 record with a 6.26 ERA and two saves in 19 games with the Nationals. He sustained his injury while pitching in Saturday's game against the Phillies.
Bill Ladson is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.