Hoeness reported himself to authorities earlier this year over a previously undeclared Swiss bank account. News of the case against Hoeness, long one of the most prominent figures in German football, emerged in April.
It caused an uproar in Germany, with even Chancellor Angela Merkel's spokesman saying that the country's leader was disappointed in him.
Ken Heidenreich, a spokesman for Munich prosecutors, declined to comment on details of the indictment, citing tax secrecy laws.
"We have filed the charges to the Munich state court," Heidenreich said. "The defence now has one month to pronounce itself."
The court will then either set a date for the trial, reject the charges or ask for further investigations before making a decision, Heidenreich said.
The court said in a statement that a decision shouldn't be expected before the end of September "in view of the volume of documents in the investigation."
In May, Bayern's supervisory board backed Hoeness to remain in the job despite the investigation against him. The club said then that Hoeness apologized and offered to temporarily give up his functions pending the outcome of his case but the board unanimously asked him to stay.
Bayern spokesman Markus Hoerwick said the club is "not saying anything about" the case.
Bayern won the Bundesliga, the Champions League and the German Cup last season. It is a strong favourite again this season under new coach Pep Guardiola.
As a player, Hoeness was a Bayern star who won the 1972 European Championship and the 1974 World Cup with West Germany and three straight European Cups — the predecessor of the Champions League — before retiring in 1979 with chronic knee problems.
He became Bayern's general manager and built the most influential career in German football. Under his guidance, Bayern built financial reserves rarely seen in debt-ridden European club football.
Hoeness, 61, was also the driving force behind Bayern's new state-of-the art Allianz Arena.
In addition to his success at Bayern, Hoeness also owns a profitable sausage factory in Nuremberg.