Russia will host the 2018 World Cup, but FIFA is facing corruption charges which includes a probe into the awarding of the competition to the country.
Putin, however, saluted Blatter after meeting with him in St Petersburg on Saturday.
"We all know the situation developing around Mr Blatter right now. I don't want to go into details but I don't believe a word about him being involved in corruption personally," Putin told Swiss broadcaster RTS.
"I think people like Mr Blatter or the heads of big international sporting federations, or the Olympic Games, deserve special recognition. If there is anyone who deserves the Nobel Prize, it's those people."
Blatter announced he would leave FIFA after 17 years at the helm, just days after his re-election for a fifth term in June.
The 79-year-old was pressured to step down following the arrest of seven FIFA officials on corruption charges by the FBI.
Swiss authorities are separately investigating how the 2018 and 2022 World Cups were awarded.