The charge relates to a $US44 million payment to German banker Gerhard Gribkowsky of Bayern Landesbank, linked to the sale of a stake in F1, the BBC reports.
The 82-year-old denies bribing Mr Gribkowsky, and says the money was intended to stop the banker from exposing him to a UK tax inquiry.
Mr Gribkowsky was sentenced to eight-and-a-half years in jail in Munich.
Speaking to the Financial Times on Wednesday, Mr Ecclestone said he had spoken to his lawyers and would be defending the case.
Mr Ecclestone has six weeks to respond to the indictment, Formula One Group said in a statement.
The charges are related to the 2006 sale of a 47% stake in F1 by Bayern Landesbank, which had acquired it from the bankrupt Kirch media group.
Mr Gribkowsky had been in charge of managing the sale to private equity group CVC Capital Partners.
CVC has since reduced its stake in a series of deals. It has not commented on the indictment.