Seven officials and associates were arrested in Zurich earlier this week, as Fifa gathered for its congress. (Read here)
Mr Blatter, 79, described the issue as "infractions" involving a marketing company operating in the Americas.
He is not named in the indictment, and denies having anything to do with an alleged $10m (£6.5m) bribe.
Asked by a reporter at a news conference whether he authorised the payment allegedly relating to the 2010 World Cup in South Africa, he said: "Definitely, that's not me."
And he again questioned the timing of the US prosecutors, saying his organisation "could have been contacted at another time" rather than just before its congress assembled.
"I don't see how Fifa should have been directly affected by this," he said.
Mr Blatter beat Prince Ali Bin al-Hussein of Jordan in Friday's election, and is starting his fifth four-year term as president.( Read here)
