The Mets say they are "surprised and deeply disappointed" to learn of the charges.
Police say the 44-year-old was observed by a White Plains police officer asleep at the wheel of a 2018 Toyota Highlander at the intersection of Fisher and South Lexington Avenues.
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They say Scott failed the Field Sobriety Test that was administered at the scene and refused to submit to a chemical breath test.
Prior to his arrest, Scott had been at the home of Mets owner Steve Cohen for a team fundraiser at which players were also in attendance, sources told ESPN's Jeff Passan.
"We were surprised and deeply disappointed to learn this morning about an alleged DUI involving Zack Scott," the Mets said in a statement. "We take this matter very seriously. Zack will not be traveling with the team for our upcoming road trip while we learn more and determine next steps."
Scott was promoted to acting general manager in January after Jared Porter was fired following an ESPN report that he sent sexually explicit, uninvited text messages and images to a female reporter in 2016 when he was working for the Chicago Cubs.
Prior to joining the Mets as assistant general manager in December, Scott spent 17 seasons in the Boston Red Sox organization.
The Mets begin an eight-game road trip Friday at the Washington Nationals.
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