Manager Luis Rojas said before Sunday's game against the Miami Marlins that Wacha felt pain in his shoulder after allowing four runs in five innings Friday.
Wacha is 1-2 with a 6.43 ERA this season. He pitched five innings of one-run ball in his debut July 27 in Boston but has allowed nine runs over nine innings in his past two starts.
Rojas said an MRI showed the inflammation, and he is not sure how much time Wacha will miss.
"I had a conversation with him about it. We're not too overly concerned," Rojas said. "It's in the back of the shoulder."
Wacha joined Marcus Stroman as the second Mets starter to get injured. Stroman tore his left calf during summer camp. He threw more than 80 pitches over five innings in a simulated game at the team's alternate site in Brooklyn, and Rojas said he will throw at least one more simulated game.
Rojas did not say who would make Wacha's next scheduled start and hinted the Mets may use an opener.
In December, Wacha signed a one-year, $3 million contract that includes $8 million in performance bonuses.
The 29-year-old Wacha shined as a rookie for the pennant-winning St. Louis Cardinals in 2013, winning National League Championship Series MVP, but has been frequently injured since, although he was an All-Star in 2015.
He had a 4.76 ERA over 126 2/3 innings last season in 24 starts and five relief appearances for St. Louis. Wacha was diagnosed with a right shoulder strain in September and did not pitch in the postseason.
To replace Wacha on their active roster, the Mets recalled catcher Ali Sanchez from the alternate site.