Blatter made dark hints about the voting process in 2000 that led to Germany hosting the 2006 World Cup rather than South Africa in an interview with Swiss mass-circulation paper Blick on Sunday.
"World Cups being bought… that reminds me of the World Cup vote in 2006, where somebody left the room at the last minute," he said.
"And so suddenly instead of 10-10, the vote stood at 10-9 in Germany's favour. I'm happy that I did not have to cast the decisive extra ballot [as FIFA president]. But, well, suddenly someone stood up and left. Perhaps in that case I was also too well-meaning and too naïve."
Franz Beckenbauer, the head of the 2006 World Cup organizing committee, rejected the claims.
"I can't accept the statements and suggestions," he said in an interview with German newspaper Bild, published Monday. "He even got the result wrong. It was 12-11 to us, not 10-9. What was decisive was that the eight Europeans voted for us."
The DFB was equally vehement in its denial. "These nebulous hints are completely baseless and seem to have been made to divert attention from the current events, which are on the record," said DFB General Secretary Helmut Sandrock.
Sandrock was referring to last week's revelations that Blatter's predecessor Joao Havelange pocketed at least 1.5 million Swiss francs (€1.25 million) in bribes from the company International Sport and Leisure (ISL) during his 24-year tenure.
Blatter insisted on Thursday he was powerless to sanction his predecessor and added that such payments were not illegal under Swiss law at the time.
"The reaction of the president of FIFA shocked me. If FIFA people, and not the lowest among them, received money and the response is that that this was not illegal at the time then we at the DFB can only distance ourselves," DFB chairman Wolfgang Niersbach said on the sidelines of a meeting of Bundesliga referees.
Blatter's hints that the vote over the 2006 world cup may not have been clean beg the question of why – as FIFA President then as now– he did not raise his suspicions of corruption at the time.
Bidding to host the World Cup is not only a matter of national pride, it also represents big business, and the decision process is often a contorted one.
In 2010, Danny Jordaan, chief executive of the organizing committee for the World Cup in South Africa, admitted that he tried to get England to withdraw from the 2006 bidding by offering Nelson Mandela's support for a 2010 English bid.