In a statement released Thursday, the Office of the Attorney General of Switzerland revealed it had opened proceedings relating to fraud, criminal mismanagement, money laundering and misappropriation against Beckenbauer, who was president of Germany's 2006 World Cup organizing committee.
Three former German Football Federation (DFB) officials are also being investigated. Theo Zwanziger, Wolfgang Niersbach are former DFB presidents and Horst Rudolf Schmidt is an ex-DFB secretary general.
The probe relates to accusations first made by German magazine "Der Spiegel"
in October 2015 that a payment of €6.7 million ($7.2 million) had been made to bribe officials of soccer's governing body FIFA in order to secure votes for Germany's 2006 bid.
Germany narrowly pipped rival candidate South Africa to host the event by 12 votes to 11 in 2000.
Beckenbauer, who won the World Cup as both player and coach, strenuously denied
any wrongdoing when the "Der Spiegel" allegations surfaced.
, who was DFB president from 2012 until November 2015, when he resigned his post, also maintained he had acted properly.
"I was always there from the first day of the 2006 World Cup bid right up until the tournament's conclusion, and in all these years not only have I always gone about my work with great passion, but I have also always worked in good faith and in a proper manner," Niersbach said on the DFB website last November
In July 2016, Niersbach was handed a one-year ban by FIFA's ethics committee who concluded
he had "failed to report findings about possible misconduct concerning the awarding of the 2006 FIFA World Cup."
The OAG stated Thursday that it believes some of the alleged crimes took place in Switzerland and its investigations are focusing on the joint financing of a 6.7 million Euro ($7.46 million) gala event that was being used as a cover for an illicit payment.
"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," the attorney general's statement explained.
"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 pretenses or concealment of the truth, thus inducing the other committee members to act in a manner that caused DFB a financial loss."
Searches were carried out in eight locations Thursday with the cooperation of police in Germany and Austria, according to the OAG.
CNN contacted the agency that represents Beckenbauer by phone but did not receive a response by time of publication.
The DFB's media director Ralf Köttker told CNN via email: "We've seen the press releases of the Swiss General Prosecutor and the media coverage. We have no further information regarding the matter."
Swiss and federal prosecutors in the US are also currently investigating successful bids by Russia and Qatar to host the 2018 and 2022 World Cup's respectively.
Meanwhile, an independent report (in German) commissioned by the DFB
earlier this year concluded that it could not prove or disprove that votes were bought during the 2006 World Cup bidding process.