The 76-year-old Swiss wrote a letter to Bild newspaper, explaining that what he was trying to say in an interview published on Sunday was that World Cup hosting decisions were always surrounded by suspicion.
In the interview with Swiss paper Sonntagsblick, Blatter remembered that Germany were awarded the tournament ahead of South Africa in 2000 after the Oceania representative on FIFA's executive committee, Charles Dempsey, abstained from voting.
"World Cups being purchased? There I am reminded of the vote for the 2006 World Cup, where somebody left the room at the last minute. And so suddenly instead of 10-10, the vote stood at 10-9 in Germany's favour," Blatter was quoted as saying, although the actual final vote was 12-11.
"I'm happy that I did not have to cast the decisive extra ballot. But, well, suddenly someone stood up and left. Perhaps in that case, I was also too well-meaning and too naive.
"No I don't suspect [that the 2006 World Cup had been purchased]. I'm making an observation."
In Tuesday's letter to Bild, Blatter said he wished to put his comments into context.
"I wanted to say that one can always find a pretext to doubt the legality of a decision," he said.
"It shows that with a World Cup hosting vote, you can always find a pretext to spin a conspiracy theory. Even in connection with Germany, which delivered a perfect World Cup, a summer fairly tale of which the whole country can be proud."
GERMAN OUTRAGE
He added: "I don't believe in conspiracy theories, but only in facts. As long as there is no concrete evidence to hand, one must and should stick by the legality of the vote.
"This applies to Germany just as much as for other countries. That is the core of my message."
Blatter's remarks caused outrage in Germany and prompted some politicians to suggest he be stripped of an honorary award he received in 2006 for services to the country.
The Bundesverdienstkreuz (Federal Cross of Merit) is Germany's highest award for individuals deemed to have served the country's common good.
"Sepp Blatter represents endemic corruption at FIFA... therefore this award should be withdrawn," Reinhard Buetikofer, a German MEP for the Greens, told newspaper Die Welt.
"If Sepp Blatter continues to not want a real investigation into bribery, than we should think about withdrawing the award," Thomas Oppermann, head of the Social Democrats parliamentary group told the same publication.
Former Germany captain and coach Franz Beckenbauer, who heads FIFA's football task force, also questioned Blatter's recollection of events in an article published in Monday's Bild.
"I cannot understand Sepp Blatter's comments and allusions. For a start, he is wrong on the result of the vote. It was 12-11 for us, not 10-9," he said.
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