The league sent out a league-wide memo saying the hats -- intended as a tribute on the 10th anniversary of the 9/11 attacks -- violated baseball's uniform regulations.
The Mets were fined for wearing the same caps in the first game in New York after the September 11, 2001 attacks and while they had planned to wear them again, did not want to draw the ire of the league a second time, The Star Ledger reported.
"MLB has put an edict out: We have to wear our regular hats," Mets manager Terry Collins said in his pregame media briefing, while wearing an FDNY hat.
The team also added in a statement, "MLB set a league-wide policy as it related to caps and uniforms for Sept. 11 and we followed the guidelines."
The league issued the same guidelines 10 years ago, but the Mets decided to wear the hats anyway.