Flores was awarded a $2.2 million salary Saturday by arbitrators Mark Irvings, Sylvia Skratek and Robert Herzog, who heard the case a day earlier. The Mets contended he should be paid $1.8 million. Flores made more than $526,000 last year and was eligible for arbitration for the first time.
He played all four infield positions last season. He hit .267, matched his career high with 16 homers and had 49 RBIs.
Fourteen players remain scheduled for hearings, which run through Feb. 17.
Perez won his hearing in 2008 and made $6.5 million instead of the team's offer of $4.7 million.