Flores injured his shoulder when he was hit with a foul ball in the May 9 game at Arizona, and was put on the 15-day disabled list on May 15. The injury was originally thought not to be serious.
As Flores intensified his preparation to return to action, he felt more pain. The Nationals sent him to Dr. James Andrews in Birmingham, Ala. on Monday.
"As we started to ramp up and rehabilitate his shoulder, it started to stress his shoulder," Washington acting general manager Mike Rizzo said.
"It's going to push back his rehabilitation greatly. It'll probably be a minimum of three months -- possibly could be for the rest of the season."
Flores, who was batting .311 with four home runs and 15 RBIs, was a Rule 5 draft choice by the Nationals from the New York Mets organization in Dec. 2006, and had rapidly progressed.
"It's a bad day for the organization," Rizzo said. "It's not a devastating injury. It's going to take time to heal."
Entering Tuesday's game with San Francisco, the Nationals have lost 18 of 21 games since Flores' injury.
"Nieves and Josh Bard are a good piece to our ballclub. They're guys we can rely on," Rizzo said. "They don't have the productivity of Jesus, but they're guys we can rely on."
Dukes, had been on the disabled list since May 18 with a strained left hamstring. He's batting .277 with four home runs and 24 RBIs.
Wells has an 0-2 record with a 6.26 ERA.