Prosecutors said there were "enough indications" the killing was either "contracted by government offices" of Russia or Russia-governed Chechnya.
Russia said Thursday it would expel two German diplomats, deepening a tit-for-tat dispute over a brazen daytime murder in a central Berlin park this summer.
It mirrors a similar move last week by Germany, which ordered the expulsion of two Russian diplomats over the killing. German prosecutors said it appeared to be contracted from within the Russian or Chechen governments.
In response, Russia's Foreign Ministry on Thursday summoned the German ambassador in Moscow, issued a formal protest over its expulsions and gave two diplomats seven days to leave the country, it said in a statement reported by The Associated Press.
The dispute revolves around the Aug. 23 murder of "Tornike K," a man German prosecutors said had previously fought alongside anti-Moscow separatists in Chechnya and "was classified and sought by Russian authorities as a terrorist."
He was walking to the mosque just before midday when he was shot twice in the head in Berlin's Tiergarten park. Often touted as Berlin's version of New York's Central Park, this tree-filled green space of 519 acres is close to the city center and tourist attractions such as the Brandenburg Gate, and is popular with local joggers.
Prosecutors have said there were "enough indications" that the killing was either "contracted by government offices of the Russian Federation or the autonomous Chechen republic as a part of the Russian Federation."
Moscow has denied any involvement in the murder.
Previously the Kremlin has accused the 40-year-old of being a member of a terror organisation called "Caucasian Emirate." And Russian President Vladimir Putin this week alleged the slain man was "a bandit" and "a murderer" and said Russia repeatedly asked Germany to extradite him, but to no avail.
Kremlin spokesman Dmitry Peskov said Thursday that the victim's alleged "participation in incredibly bloody terrorist acts and mass murders" in Russia had been established by Russian law enforcement agencies, AP said.
Meanwhile, Russia's only aircraft carrier was ablaze Thursday injuring two service members, Russian military officials told the AP. The Admiral Kuznetsov was docked in Murmansk in northern Russia for an upgrade when the fire started during welding work Thursday morning.