ReutersBlatter said in Switzerland's Blick newspaper that the voting procedure which eventually saw Germany given the World Cup by just one vote was suspicious since one delegate left the room before votes were cast.
However, he has now explained that what he meant by that is not that he felt the vote was rigged, but that there is "always a reason to find some kind of conspiracy theory".
"What I meant to say was that you can always find a smokescreen to doubt the legitimacy of a decision," he wrote.
"When asked if I suspected that the 2006 World Cup had been bought, I responded: 'No, I don't presume anything, I am stating facts' and this means that somebody did indeed leave the room during the vote, which Germany won by one vote.
"I don't believe in conspiracy theories - I only believe in facts.
"As long as there is no clear proof that something illicit was done at any World Cup vote, then you have got to adhere to the legality of the vote. This applies to Germany like it applies to every other nation. That is the main point I was making."
Nevertheless, Blatter's remarks have caused outrage in Germany, with leading politicians calling for him to have his Order of Merit of the Federal Republic of Germany revoked.
He received the accolade in 2006 for his services to the country having awarded Germany the World Cup, but spokesperson for Germany's Green party, Reinhard Butikofer, told the Welt newspaper that he should now be forced to hand it back. "Sepp Blatter stands for the endemic corruption in FIFA," he said. "Therefore, his Order of Merit should be withdrawn."
Blatter is currently in the focus of a bribery scandal with calls for him to step down. German Football League president Dr Reinhard Rauball called the Swiss last weekend to advise him to resign from his position, prompting Blatter's remarks in the Blick newspaper on Sunday.
