The 28-year-old suffered the problem in his right leg shortly before half-time in the 1-0 World Cup qualifier win over Armenia on Tuesday night.
A statement on Mainz's official club website said: "Niki Zimling has returned with a muscular injury from his international duty for Denmark in Armenia.
"The Mainz midfielder has a hamstring injury suffered in his right calf and was forced off injured shortly before half-time in Yerevan.
"Zimling is not expected to be available for Mainz in the next three weeks."
Mainz are currently fifth in the Bundesliga after the opening four league games of the season.