As members of that cup’s organizing committee, they are suspected of fraud, criminal mismanagement, money laundering and misappropriation, prosecutors say.
Some of the alleged crimes were carried out on Swiss territory.
Franz Beckenbauer, who headed the bid, has previously denied corruption.
In October 2015, he said he had made a “mistake” in the bidding process to host the competition in 2000 but denied votes had been bought.
In March 2016, soccer’s world governing body FIFA began looking into six men for their part in Germany winning the rights to host the 2006 cup.
Premises were searched in eight undisclosed locations on September 1 with the co-operation of the Austrian and German authorities, the prosecutors said.
Franz Beckenbauer’s home in Austria was among the properties searched, according to the AP.
Several suspects were also questioned, the prosecutors added.
Germany beat South Africa 12-11 in the World Cup vote, which took place in July 2000.
The Swiss investigation centers on the use of 7 million euros ($7.8 million), later reduced to 6.7 million euros, earmarked for a gala event.
In a statement, Swiss prosecutors said: “It is suspected that the suspects knew that this sum was not being used to fund the gala event, but instead to repay a debt that was not owed by the DFB.
“In particular, it is suspected that the suspects willfully misled their fellow members of the executive board of the organizing committee for the 2006 World Cup.
“This was presumably done by the use of false pretences or concealment of the truth, thus inducing the other committee members to act in a manner that caused DFB a financial loss.”
No further details were given.
Earlier today, Germany’s Spiegel magazine reported the investigation centered on payments made from 2002 to 2005.
In October 2015, Franz Beckenbauer said he did not give “money to anyone in order to buy votes”.
However, in a statement, he said: “In order to get a subsidy from FIFA [for the organization 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-organizing committee, bear the responsibility of this mistake.”
Swiss prosecutors named four suspects on September 1:
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