The Indians recalled right-hander Adam Plutko from Triple-A Columbus to take his spot on the roster.
Indians manager Terry Francona said Naquin's hip had been bothering him, and it started to hurt Friday when he was doing outfield drills.
"So we got him scanned and the doctor is just not comfortable releasing him to play," Francona said Friday night. "So we're going to send him back to Cleveland so he can get worked up there and see what's going on."
Naquin is hitting .263 with three homers and 23 RBIs in 61 games.
Naquin's injury leaves the Indians thin in the outfield. They are without Lonnie Chisenhall, who is out eight to 10 weeks with a left calf strain, and Bradley Zimmer, who underwent surgery on his right shoulder and is done for the season.