Video on social media showed Mr. Met walking down a tunnel at the ballpark, turning around and giving the middle finger to the fans. It was unclear what, if anything, the fans said to the mascot before he made the gesture.
"We apologize for the inappropriate action of this employee," the Mets later said in a statement posted to their Twitter account. "We do not condone this type of behavior. We are dealing with this matter internally."
A Mets official told The Associated Press more than one person wears the Mr. Met costume during each season, and the person who wore it Wednesday night will not work in the costume again.
The team said a different person was doing Mr. Met duty for Thursday's game against Milwaukee. The mascot was at his spot before the game, posing for pictures, signing autographs and high-fiving fans young and old.
Mr. Met, known for an oversize head with baseball seams, is among the sport's most recognized mascots. Technically, he has only four digits on each hand -- three fingers and a thumb.
Mr. Met has been the Mets' live mascot since 1964. It has an official Twitter account, with almost 50,000 followers. And it was in the headlines previously this season, with a friendly, online back-and-forth with Mets right-hander Noah Syndergaard.
On the field Wednesday night, Mets right-hander Jacob deGrom was pounded for seven runs on eight hits in a loss to a Brewers team that entered the night with just two wins in its previous nine games. An announced attendance of 26,517 took in the game as the Mets dropped to 23-28 on the year.
In an earlier flap, after a win over the Miami Marlins on May 5, the Mets tweeted a photograph of T.J. Rivera wearing the star-of-the-game crown in their clubhouse, and the background included the locker of backup catcher Kevin Plawecki and a clearly visible sex toy. Plawecki attributed the incident to clubhouse pranksters.
Then, Mets pitcher Matt Harvey didn't show up for the next day's game after a late night on the town, causing the team to suspend him for three days.
Information from The Associated Press was used in this report.