The idea of a regional Super League "goes against the principles of FIFA and will not happen," said Blatter, reports Xinhua.
Clubs should organise club competitions but not to cross national borders, Blatter said during his visit to the Russian city of St. Petersburg.
"It's the policy of FIFA and the whole world football family. We will never reconsider the boundaries of national leagues," he added.
Russian clubs such as CSKA Moscow, Zenit St. Petersburg and Anzhi Makhachkala back the plan of forming a regional Super League.
Blatter, who was visiting Russia to attend the 21st CIS and Baltic Cup matches, discussed Russia's preparations for the 2018 World Cup with President Vladimir Putin Saturday.
According to Putin, the FIFA president's presence at the CIS and Baltic Cup "adds authority to this tournament".