Earlier in March, football's world governing body FIFA began looking into six men for their part in Germany winning the rights to host the 2006 World Cup.
Swiss prosecutors said they have launched their own investigations, linked to that of FIFA, BBC reported on Thursday.
Beckenbauer, who headed Germany's bid, has denied corruption.
Last October, he said he made a "mistake" in the bidding process to host the competition, but denied that votes were bought.
Germany beat South Africa 12-11 in the vote, which took place in July 2000.
Germany's Spiegel magazine reported on Thursday that the investigation centred on payments made from 2002-2005 that added up to more than 10 million Swiss francs (7.7 million euros; $10.2 million).
In March, it emerged that six men being investigated by FIFA's ethics committee, Franz Beckenbauer, who was the former vice-president of the German Football Association (DFB), president of the 2006 World Cup local organising committee (LOC) and former member of the FIFA executive committee.
Wolfgang Niersbach, who was the former president of the DFB, vice-president of the LOC and current member of the FIFA and UEFA executive committees. Helmut Sandrock, who was the former secretary general of the DFB and tournament director of the LOC.
Theo Zwanziger who was the former president of the DFB, vice-president of the LOC and former member of the FIFA and UEFA executive committees.
Horst Schmidt, who was the former secretary general of the DFB and vice-president of the LOC and Stefan Hans, who was the former chief financial officer of the DFB and chief financial officer of the LOC.
Last October, Beckenbauer said he did not give "money to anyone in order to buy votes".
But later in a statement, he said, "In order to get a subsidy from FIFA (for the organisation of the 2006 World Cup) those involved went ahead with a proposal from the FIFA finance commission that in today's eyes should have been rejected.
"I, as president of the then-organising committee bear the responsibility of this mistake."
He captained West Germany to victory as hosts at the 1974 World Cup and was coach when they next lifted the trophy, in Italy 16 years later.
The former defender went on to manage French side Marseille and German giants Bayern Munich, where he is now honorary president.
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