Manager Terry Collins said Wednesday that Niese felt pain in the triceps area after throwing live batting practice earlier this week.
"It's a precaution right now. But any time you're sending someone for an MRI, obviously there's going to be a concern until you get the reading back," Collins said.
"He just said he's got a little discomfort in there. So we're going to go have it looked at," he said.
Niese has been expected to be the Mets' starter on opening day.
"Batting practice started and he felt fine," Collins said. "And then he threw his second 20 pitches the other day. He just said at the end of it, 'Geez, my arm's just dead. Like, it's dead.'"
Collins said Niese previously felt some pain in camp and was switched from throwing off the mound to playing long toss.
"That forces you to get your arm a little higher. And he felt good," Collins said.
But after Niese felt the problem during BP, the Mets sent him back home to be examined.
Niese went 8-8 with a 3.71 ERA in 24 starts for the Mets in 2013. He was on the disabled list from June 21 to Aug. 11 with a partial tear in his rotator cuff.