Right-hander Jose Butto, who has a 6-6 record and 4.22 ERA in 22 appearances for Double-A Binghamton and Triple-A Syracuse, will replace him for Sunday's game against Philadelphia.
Walker (10-3, 3.36 ERA) lasted only two-plus innings in Tuesday's loss to Atlanta, leaving with back spasms. He was visibly wincing after running to cover first base on a ground ball and said after the game that his back "started getting tight" as he walked back to the dugout.
Showalter said Walker possibly could return to the rotation against the Yankees on Tuesday.
The Mets have a three-game lead over the Braves in the NL East.
The Associated Press contributed to this report.