This is Zimmerman's second trip to the DL since arriving in the majors in 2005. The move Tuesday is retroactive to Sunday.
"It's frustrating," Zimmerman said. "Nobody ever wants to do it. But the important thing is to get healthy and there's a long season ahead."
Zimmerman is hitting .357 with a triple, homer and four RBIs in eight games.
Nationals manager Jim Riggleman said he doesn't know how long it will take the injury to heal, but he hopes to have him active in about 10 days -- though it could be much longer.
"We hope for 10, but we're certainly not going to rush the process," Riggleman said.
The injury first occurred during spring training, although Zimmerman said he couldn't pinpoint the exact timing. It was re-aggravated last week and he sat Sunday against the Mets.
"It bugged me a little bit at the beginning of the season, but I could still play and be effective," Zimmerman said. "It got to the point in New York where I wasn't going to be a good player if I continued to play with it."
Flores gives the Nationals three catchers, along with Ivan Rodriguez and Wilson Ramos. Riggleman said Flores would be used primarily as a pinch hitter. He missed all of last season after undergoing shoulder surgery and hasn't played in the major leagues since September 2009.
"It's been a long time," Flores said. "I'm happy. I feel the work I've been doing the last couple years worked out for me."
Washington is also without two other regular starters for Tuesday night's game against the Phillies. First baseman Adam LaRoche has a groin injury and outfielder Michael Morse will sit with flulike symptoms, although Riggleman said both are available to pinch hit if necessary.
Riggleman said the team's trainers wanted to hold LaRoche out a few more days, although LaRoche said he wanted to be on the field.
"If I was making out the lineup, my name would be in it," LaRoche said. "That being said, I don't always make the smartest decisions."'