PHOENIX -- Right-hander Zack Wheeler's return to the New York Mets might have to wait until 2017.

In the latest setback during his quest to return from Tommy John surgery, Wheeler was diagnosed by Dr. James Andrews on Wednesday with a mildly strained flexor muscle. Wheeler will stop throwing for at least two weeks and will receive a platelet-rich plasma injection.

Mets assistant general manager John Ricco did not declare that Wheeler's latest setback will prevent him from reaching the majors this season, but he noted time is no longer on Wheeler's side.

"The reality is two weeks takes you to the beginning of September," Ricco said. "So I'm not going to jump to that at this point, but the clock is certainly ticking."

Zack Wheeler's latest setback in his recovery from Tommy John surgery has put his 2016 season in jeopardy. Rich Schultz/Getty Images

Wheeler underwent Tommy John surgery on March 24, 2015.

The Mets originally eyed July 1 for Wheeler's return to the majors, but three setbacks have seriously derailed those plans.

Wheeler underwent a second surgery in April to remove an undissolved stitch from his original procedure.

Then, as Wheeler was nearing a rehab assignment in June, he experienced elbow discomfort. Wheeler was diagnosed by team doctor David Altchek at the time with nerve irritation and given a cortisone injection.

And after pitching an inning for Class A St. Lucie on Aug. 6 in his first rehab outing, Wheeler complained of renewed elbow discomfort. An appointment was scheduled with Andrews to have another set of qualified eyes evaluate his persistent discomfort.

"Obviously, the good news was the ligament is intact," Ricco said. "There's no problem there. So the muscle strain is, I guess, the cause for some of the elbow soreness."

Wheeler has not pitched in a major league game since Sept. 25, 2014.

"We started out the year very confident that he would, at some time in July, be back," Mets manager Terry Collins said. "Then, as the summer proceeded on where he never felt comfortable -- especially in the last month, where every time it seemed like he got on the mound there was discomfort -- we all of a sudden realized this may not be what we thought was going to happen.

"We're very disappointed. We feel bad for Zack. I know he certainly wanted to pitch and was looking forward to pitching. But nobody knows how he feels any better than he does. I just hope that with the rest and the recuperation, he can come back in the future and be effective."

If it is ultimately determined that Wheeler cannot contribute in the majors this season, it is unresolved whether Wheeler will continue to pitch into October to try to demonstrate his health or whether he will be shut down, according to Ricco.

"That's something the doctors and [general manager] Sandy [Alderson] will discuss with Zack and figure out what the best course is to head into the offseason," Ricco said. "If you remember back to some guys like Johan [Santana] that one year, we tried to make sure we got him out there and got him on the mound so he headed into the offseason feeling like he was going to be ready. I don't know how they'll map this one out. That remains to be decided."

The Mets really could use Wheeler. With Matt Harvey sidelined for the remainder of the season with thoracic outlet syndrome, Logan Verrett originally stepped into that rotation slot and went 0-3 with a 7.18 ERA in seven starts. The Mets will now try Jonathon Niese in that role on Wednesday night against the Arizona Diamondbacks.

As for whether the Mets can even count on Wheeler for 2017, Collins said, "I think you've got to certainly prepare yourself for the fact he might be one of those guys that for some reason doesn't bounce back like you'd hope. I know Sandy will certainly prepare for that. It's very discouraging to hear today that he's got to be shut down."

Despite the Wheeler news, the Mets are making some strides on the injury front. Left fielder Yoenis Cespedes (quadriceps) and shortstop Asdrubal Cabrera (knee) both continued rehab assignments with Class A St. Lucie on Wednesday. The Mets believe Cespedes will be activated from the disabled list on Friday in San Francisco and Cabrera will return by the end of the weekend. Outfielder Justin Ruggiano (hamstring), who is rehabbing with Triple-A Las Vegas, also is due back any day.

Second baseman Neil Walker, meanwhile, will be sidelined for a second straight game on Wednesday with lower-back stiffness.