The Swiss Public Prosecutor's Office (MPC) is investigating whether German football officials used a secret slush fund to buy votes in support of their successful bid to host the 2006 World Cup and has brought charges against four officials.
In addition to Beckenbauer, who was president of Germany's bid committee, the MPC charged two former presidents of the German Football Association (DFB), Theo Zwanziger and Wolfgang Niersbach, and a former Secretary General of FIFA, Urs Linsi, who is Swiss.
The 74-year-old Beckenbauer, a World Cup winner for Germany as a player and as a coach, lives in Austria.
In August, the MPC decided to separate the proceedings against Beckenbauer because of his health.
The German weekly Der Spiegel reported last summer that Beckenbauer's health had "deteriorated significantly" and that "his judgement and memory were impaired".
The three other accused objected to separating Beckenbauer's case, but their request was dismissed by the Complaints Chamber of the Swiss Federal Criminal.
In their decision, published on Tuesday, the chamber said that the Austrian authorities had given an expert three months to produce a medical report.
The corruption investigation concerns the possible use by Germany of a secret fund of €6.7 million (around 7 million dollars) to buy votes within FIFA, particularly that of Qatar, and to beat South Africa in the vote to host the World Cup.
The money was allegedly provided by the late Robert Louis-Dreyfus, head of German sportswear giant Adidas, at Beckenbauer's request.
According to Der Spiegel, the DFB had borrowed the cash to buy the votes for the German bid.
The funds were originally reported to have been transferred for a World Cup opening gala, an event which never took place.
The three accused Germans are also being investigated at home for tax fraud. After the scandal erupted, Frankfurt's tax office subsequently found that the German football federation (DFB) did not appropriately account for the 6.7 million euros, and fined it 19.2 million euros.