The charges reportedly relate to a Swiss bank account that Hoeness declared in January this year.
The account was previously undeclared and reports emanating from Germany allege that the 61-year-old failed to pay capital gains tax.
"The Munich II prosecutor's office has completed the investigation and has filed charges with the respective court," the Munich regional court said in a statement released to the media on Tuesday.
Hoeness now reportedly has one month to respond to the charges before a decision is made on whether the case should go to trial.
The news comes after a lengthy inquiry by German prosecutors.
Hoeness offered to walk away from his position with Bayern in May while the inquiry was ongoing, but the UEFA Champions League winners refused to accept his resignation and have stood by the former West Germany international.
The case has created plenty of headlines in Germany, with chancellor Angela Merkel quoted as being "disappointed" with Hoeness' alleged conduct.
Hoeness made more than 200 appearances for Bayern during the 1970's before taking up the role of general manager and then becoming president of the Bavarian giants.
