The 34-year-old said Wednesday that he has soreness in the back of his left knee and will undergo an MRI.
"It started when I started really ramping things up, started getting into high-end speed stuff," Lowrie said.
Lowrie signed a two-year, $20 million deal with the Mets this offseason.
The switch-hitter is coming off his first All-Star appearance. In his 11th major league season, Lowrie set career highs last year for Oakland with 23 homers, 99 RBIs, 78 walks and 128 strikeouts, hitting .267.
Playing a lot could pay off for Lowrie as well. He can earn a $500,000 performance bonus during each season of his deal if he makes 550 plate appearances. He would get a $500,000 assignment bonus each time he is traded and also can earn award bonuses.
Lowrie said that he noticed the problem recently while running and it's been pretty much constant discomfort since then.
"It's one of those things we've got to get checked out," he said.
Information from The Associated Press was used in this report.