Niese is expected to have an MRI exam on Monday, and it's unclear when he might pitch again.
"It's the back of the elbow, which is good," Niese said. "I'm almost 100 percent sure it's nothing serious."
Shoulder soreness slowed Niese earlier this spring, and Sunday marked only his second Grapefruit League start. Following his first outing, Niese was optimistic he could be ready for opening day, but now that appears unlikely.
"It's frustrating," Niese said.
Niese, who started the Mets' season opener last year, allowed two runs in two innings and didn't come out of the dugout for the third. He gave up three hits and one walk, throwing 24 of his 35 pitches for strikes.
"He actually wanted to go back in and pitch," general manager Sandy Alderson said in Las Vegas, where the Mets were playing another game. "Obviously as it closer to opening day, it becomes more problematic. Hopefully, it's nothing serious. The positives, it's not his shoulder. It raises the issue of our starting pitching depth. The fact that we have it is reassuring."
Niese was sidelined last June with a partially torn rotator cuff. He returned in August, going 5-2 with a 3.00 ERA the rest of the way to finish 8-8 with a 3.
"We got two weeks to go. I said go back to New York and get it done. If you're fine, you'll be back in five days. You always worry with a pitcher," manager Terry Collins said in Las Vegas. "We need him."