The newspaper said Beckenbauer, 70, was still at his home in Salzburg, Austria on when authorities carried out a two-hour search, but travelled to a clinic in southern Germany on Friday to prepare for the long-scheduled surgery.
The Swiss Attorney General's office last week launched an investigation into allegations of fraud, criminal mismanagement, money laundering and misappropriation involving Beckenbauer and two former presidents of Germany's football federation (DFB) in connection with its successful bid for the 2006 World Cup.
Beckenbauer - who led West Germany to World Cup wins as both player and manager - has previously admitted to making mistakes but has denied wrongdoing.
Widely regarded as one of the game's finest players, he captained the West Germany team that won the 1974 World Cup and was coach when they won again in 1990.
(Reporting by Andrea Shalal; Editing by Toby Chopra)
