The centre-back limped off the pitch in the 18th minute and was replaced by Alexander Hack as the Zerofivers lost 2-0 to Koln in their last Bundesliga game of the season.
The 28-year-old defender was scheduled to join the Super Eagles in Corsica for preparation ahead of the 2019 African Cup of Nations qualifiers against South Africa and might be a doubt for the crucial fixture on June 10.
“Due to an injury he picked up in the final game of the season, @LeonBalogun has had to withdraw from international duty with Nigeria,” the club tweeted.
Due to an injury he picked up in the final game of the season, @LeonBalogun has had to withdraw from international duty with Nigeria. pic.twitter.com/KEQD0DPvvj — Mainz 05 English (@Mainz05en) May 23, 2017
The Super Eagles commenced training with 12 available players on Wednesday morning.