An investigation is still underway and no charges have yet been filed, police said.
The Saxon State Criminal Police Office said the seizure of 50,000 bitcoins could be the biggest to date of its kind in Germany.
Police said they were investigating two men, aged 40 and 37, who are suspected of running a piracy website until the end of 2013. Authorities allege the men bought bitcoins from the money they earned from the portal.
They added that their investigation was into suspected unauthorized commercial exploitation of copyrighted works and subsequent commercial money laundering.
Suspects transfer bitcoins to federal agency
The seizure came after the "accused voluntarily transferred" the bitcoins to an official wallet of the Federal Criminal Police Office (BKA), police added in a statement.
The BKA did not provide further details about the transfer, but investigators cited by German news agency dpa said no decisions had been made regarding cashing in the bitcoins.
