NEW YORK — Mets pitcher Sean Manaea complained of elbow discomfort following his most recent minor league rehab outing, and his return to New York’s injury-depleted rotation will be delayed.

Manaea had an MRI on Monday that showed loose bodies in his left elbow. He received a cortisone shot and was shut down from throwing for two to three days.

“They’re telling me that he should be fine for the rest of the year. But again, we’ll see what happens there,” manager Carlos Mendoza said Tuesday.

New York’s top starter last season, Manaea has been sidelined since spring training by a right oblique strain. After a gradual progression, the left-hander pitched well for 5 1/3 innings last Friday at Triple-A Syracuse and was expected to come off the 60-day injured list in early July after making one more rehab start this week.

Instead, he was returned from his rehab assignment Tuesday and won’t pitch in the minors again until at least next week.

“After what just developed here after the last outing, we’ve got to take it one outing at a time,” Mendoza said.

The skidding Mets had been counting on Manaea’s impending return to help replenish a rotation minus ace Kodai Senga (right hamstring strain) and fellow right-hander Tylor Megill (elbow sprain). They are among nine Mets pitchers on the injured list.

The team did get a starter back Tuesday, when veteran right-hander Frankie Montas was reinstated from the 60-day IL to start against Atlanta in his Mets debut.

Right-handed reliever Chris Devenski was optioned to Triple-A following Monday night’s loss to the Braves, and designated hitter Jesse Winker (right oblique strain) was transferred to the 60-day injured list.

The goal is for Winker to begin a minor league rehab assignment by the end of this weekend, Mendoza said. He’s been out since getting hurt on May 4.

The 32-year-old Montas, sidelined all season by a right lat strain, signed a two-year, $34 million contract as a free agent in December. He was roughed up consistently in six minor league rehab appearances, compiling a 12.05 ERA.

New York had lost nine of 10 heading into Tuesday night, dropping the Mets 1 1/2 games behind first-place Philadelphia in the NL East.