The corpse of the wolf, shot dead and then its head cut off – possibly as a trophy – was found on the border between Brandenburg and Saxony in the week after Christmas.
It comes after a similar grisly find of a decapitated wolf in Saxony in August, sparking fears the same culprit may be responsible.
“We are taking this very seriously”, a police spokesman for Brandenburg police told Berliner Morgenpost.
Wild wolves were reintroduced into Brandenburg – the state surrounding Berlin – at the start of the millennium, and have become a trophy among hunters.
That is despite being a protected species, with infringements carrying up to a 50,000 euro fine.
The desecrated corpse was found on Boxing Day, whilst another wolf was found shot and then decapitated in August near the town of Lieberose, in Saxony.
The corpse has been taken to the Liebniz Institute for Zoo and Wildlife Research in Berlin for further research, but police confirmed it was shot first.
Police are working with both the Environmental Agency and their Saxony colleagues, the spokesman said.
Any such killing violates the Endangered Species Act, although police stressed there was no concrete evidence yet to link the two crimes, beyond their similar nature, and are appealing to the public for help.
Markus Barthen, of the German Nature Protection Association (NABU), welcomed the police investigation, and warned: “The wolf is a part of nature. Those that act illegally against them, must realise that their actions will not be tolerated.”
There are estimated to be 12 packs of wolves living wild in Brandenburg.
Some 14 wolves have been hunted and killed illegally since 2000, according to NABU, including three in 2014 in Brandenburg.