Michel Temer, who reportedly denies any wrongdoing, could be suspended from office for six months if he has to face trial.
Brazil’s attorney general’s office said the country’s top prosecutor, Rodrigo Janot, has filed the charges.
Janot has accused Temer of paying hush funds to a former speaker of the lower Chamber of Deputies and to an operator of his political group, and alleges that Temer is the criminal organisation operating in Brazil’s Congress and executive.
He also accused Temer of bribery in July, but lawmakers refused to allow the proceedings to go forward.
Six heavyweight political allies were accused alongside the president.
He will only go on trial if two thirds of Brazil’s lower house votes to suspend him from office.
However, it is suspected he has enough support in Congress to avoid a trial.