German football has been engulfed by claims that a €6.7-million euro ($7.2 million) payment to Fifa was used to purchase the votes of four members of FIFA's executive committee in 2000 — days before Germany narrowly won the right to host the 2006 finals.
Beckenbauer, like the former chief of Germany's football association Wolfgang Niersbach, has insisted that no bribery was involved and that the sum had to be paid to Fifa in order to obtain a bigger grant from world football's governing body.
But Blatter called the claim "absurd" in an interview with Der Spiegel magazine.
"Pay money to get money? No. There's no such thing at Fifa," said the 79-year-old, adding that the German Football Association (DFB) "must clear up this affair".
"There are always documents for anything to do with money. If the DFB is unable to provide documents, then it should approach Fifa to get to the bottom of the issue," he said.
Beckenbauer, who led Germany's successful bid for the World Cup, is under investigation by Fifa, although the governing body has not revealed why he was being probed.
Blatter himself is suspended by the organization he has headed for 17 years, and faces a hearing at the ethics committee next week over allegations of corruption.
The graft row against the Blatter had erupted over a $2-million payment made by Fifa to Uefa chief Michel Platini in 2011.
Platini has claimed it was for work done a decade earlier. But both men now face lifetime bans from football over the case.
Blatter told Spiegel however that he was "convinced he would not be punished".
Separately, Swiss prosecutors have said they were targeting Blatter for possible criminal mismanagement during his tenure as Fifa's president, including signing off on a disputed TV rights deal.