Cespedes was not named in the line-up to face the Braves, but the outfielder was due to be at Truist Park.
The 34-year-old did not report to the ballpark and general manager Brodie Van Wagenen says the Mets were not able to get hold of him.
"He did not reach out to management with any explanation for his absence." Van Wagenen said
"Yoenis Cespedes has not reported to the ballpark today. He did not reach out to management for an explanation and any attempts to reach Cespedes have been unsuccessful" pic.twitter.com/RHL4tXnUkE— SNY (@SNYtv) August 2, 2020
Two-time All Star Cespedes has been beset by injury problems but was on the Mets' Opening-Day roster following two years on the sidelines.
He hit the winning home run against the Braves in a dream return and has featured in eight of the Mets' first nine games.
The New York Post reported Cespedes fractured his ankle last year after stepping into a hole during a run-in with a wild boar.