"I confirm that an operation is underway in this context," a spokesman for the Swiss authorities in Bern told AFP by email.
Swiss authorities also confirmed that last year they had already opened criminal proceedings against former German Football Association (DFB) presidents Theo Zwanziger and Wolfgang Niersbach, as well as former DFB general secretary Horst R. Schmidt.
Niersbach resigned as president of DFB in November amid the allegations, saying he took "political responsibility" for the graft claims, but admitting no personal guilt.
Zwanziger said following the news of the investigation that it "has no substance".
"It is very clear that I did not know anything about these events," he said, adding that there had been no search of his home.
German magazine Der Spiegel first reported that Beckenbauer, who captained Germany to the 1974 World Cup title and coached the side which won Italia 1990, faces the threat of prosecution.
Der Spiegel said the Swiss are investigating Beckenbauer concerning allegations of both mismanagement and money laundering.
In October 2015, the magazine claimed a secret fund of 10 million Swiss francs (€6.7 million) 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 tournament.
The money allegedly came from the late Robert Louis-Dreyfus, ex-boss of Adidas, at Beckenbauer's request.
Beckenbauer and Niersbach have 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.
In May, an independent inquiry commissioned by the German Football Association (DFB) said it could not rule out that Germany bought votes to secure the 2006 World Cup.
Beckenbauer, 70, who was head of the organizing committee for the 2006 finals, has always denied any wrongdoing.
"I had nothing to do with it," Beckenbauer told German daily in Bild March when asked about the allegations. Instead, he pinned blame on his now deceased lawyer, Robert Schwan.
"Robert handled everything for me - from changing the light bulbs to important contracts," said Beckenbauer.
In football-mad Germany, Beckenbauer is regarded as an idol, but the scandal has damaged his image, something which clearly irks him.
"I am not going to allow my life's work to be ruined," he insisted previously to Bild.
"I was a world champion as a player and coach. I helped bring the World Cup to Germany, which was a great success. It remains 'the summer fairytale'."
"In hindsight, I might have made mistakes. Hindsight is easier than foresight."