Speaking in St. Petersburg, Sepp Blatter said the creation of a CIS league was "against FIFA principles" and could "bring disarray."
Top clubs like Zenit St. Petersburg and Ukraine's Dynamo Kyiv have proposed forming a post-Soviet CIS league, featuring the best clubs from the region, as a way of boosting exposure.
But critics, including the Russian football federation, say the system would damage existing leagues.
Blatter is in Russia to attend the annual Commonwealth Cup tournament featuring under-21 teams from the former Soviet Union.
He also met with Russian President Vladimir Putin to discuss the country's preparations to host the 2018 World Cup.