After playing a second full rehab game in the Florida State League on Thursday night, Pagan complained of pain in the strained left oblique that sent him to the disabled list on April 22, manager Terry Collins said.
Pagan returned to New York for an MRI, which showed tenderness on his left side, Mets spokesman Jay Horwitz said after a 6-3 win over the Los Angeles Dodgers.
"He's going to be held back from baseball activities until he's pain free and probably go back to Florida on Sunday," Horwitz said.
Clearly, a recurrence of discomfort requires a shutdown period, meaning Pagan may now be at least a few weeks from returning.
"We need him back, and we want him back," Collins said. "It certainly just prolongs the whole thing. But ultimately we've got to make sure he's ready to play, and he's not."
Josh Thole, who has struggled defensively, returned behind the plate Friday after not playing the field for two games. Collins said Thole established a good rapport with pitcher Jonathon Niese in a loss to Philadelphia's Roy Halladay last weekend.