The eight-time All-Star was sidelined earlier this year for almost seven weeks with a left oblique injury but the Mets had hoped he would return to finish the season strong.
Scherzer said it was not a "significant injury", with Mets manager Buck Showalter expecting him to miss one or two starts as part of a series of roster moves for the side.
"That's the first and foremost thing - this is not a significant injury," Scherzer said.
"This is more that I'm going to miss one start - we knew that - and then once the ball's out of my court, the team's gotta do what they gotta do for roster moves.
"I don't have one specific spot that you can point to where that hurts. It's just general fatigue on the whole left side."
Three-time Cy Young Award winner Scherzer has a 9-4 record this season, with a 2.26 ERA.