"In addition to the Libor and Euribor interest rates, BaFin is looking at other bench-marking processes such as gold and silver price fixing at individual banks," the watchdog said in a statement.
"The probe was launched a number of months ago and is still ongoing," BaFin said, adding that for confidentiality reasons it could not say which banks are concerned or the state of the investigation.
The prices of gold and silver are fixed twice-daily in London, acting as a benchmark for other precious metal markets.
The gold price is fixed via a teleconference between five banks, Bank of Nova Scotia, Barclays, HSBC, Deutsche Bank and Societe Generale, while the silver price is fixed by Deutsche Bank, HSBC and Bank of Novia Scotia.
Libor and Euribor are estimates of the rates at which banks lend money to each other and are based on estimates provided by a panel of banks.
The index is used to set rates on a multitude of contracts and financial products.
But the manipulation of such indices has already led to significant fines for banks.
The scandal erupted last year when Barclays was fined €339 million by British and US regulators for attempted manipulation of interbank rates between 2005 and 2009.