Beckenbauer, 70, is under investigation with three other members of the 2006 World Cup organising committee -- Hans-Rudolf Schmidt, Theo Zwanziger and Wolfgang Niersbach -- said the Office of the Attorney General of Switzerland.
"The proceedings relate in particular to allegations of fraud, criminal mismanagement, money laundering and misappropriation," the office said in a statement.
"The suspects were members of the executive board of the organising committee for the 2006 World Cup in Germany."
All four were members of Germany's World Cup organising committee, with Beckenbauer its president.
Beckenbauer captained Germany to the 1974 World Cup and coached the side that won the trophy in Italy in 1990.
German magazine Der Spiegel claimed in October 2015 a secret fund of 10 million Swiss francs was used to buy the hosting rights of the 2006 World Cup.
The money allegedly came from the late Robert Louis-Dreyfus, ex-boss of Adidas, at Beckenbauer's request, and was handed over in 2000, just before Germany were awarded the 2006 finals by a narrow vote.
Beckenbauer has always denied any wrongdoing.
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