Putin said in televised comments Thursday that it is "odd" that the probe was launched at the request of US officials for crimes which do not involve its citizens and did not happen in the United States.
In a separate probe, Swiss prosecutors are investigating the awarding of the 2018 World Cup to Russia and the 2022 tournament to Qatar.
Putin described Wednesday's pre-dawn arrests of seven soccer officials in Zurich as "yet another evident attempt to derail Mr. Blatter's re-election as FIFA president."
Putin added he is aware of "the pressure" on Sepp Blatter for his support of Russia hosting the World Cup, the Associated Press reported.