Russian Federation scoffed at the suggestion, with Kremlin spokesman Dmitry Peskov telling reporters there are "no serious suspicions there, and there can't be".
"There are sufficient factual grounds to suggest that the killing. was carried out either on behalf of state agencies of the Russian Federation or those of the Autonomous Chechen Republic, as part of the Russian Federation", Germany's federal prosecutor said on Wednesday.
Russia's top diplomat, Foreign Minister Sergei Lavrov, said the country was preparing its official response.
Russia's foreign ministry says the expulsion of two Russian diplomats from Germany over the August slaying of a Georgian man in Berlin is "groundless" and "unfriendly".
Khangoshvili survived an earlier assassination attempt in the Georgian capital, Tbilisi, in 2015, after which he fled to Ukraine where he is believed to have worked closely with the authorities against Russian interests.
The German Foreign Ministry also announced that two employees at Russia's embassy in Berlin had been designated personae non grate and were expelled.
A Georgian national, Khangoshvili fought in the second Chechen war against Russian forces in the North Caucasus in the period 2001-2005.
He added that now that the Russian state has been implicated in the crime, Moscow should start cooperating in the case "to avoid a further loss of confidence". Prosecutors said he also went by the alias Vadim S., and German and global news outlets have reported he had links to organized crime in Russian Federation.
Vadim S is an alias, prosecutors say.
In their investigation, they found that Zao Rust had only one employee in 2018 and on April 10, 2019, was listed as being in "reorganization".
But the company was not operational and a fax number for the firm was registered to another company belonging to Russia's defence ministry. Upon arrival, he extended his room to August 26, but left at 8 a.m. on August 22 and never returned, prosecutors said.
The case came almost 18 months after former Russian spy Sergei Skripal and his daughter Yulia were poisoned with the Russian nerve agent Novichok in Britain, sparking global outrage.
Krasikov was the subject of an worldwide arrest warrant issued by Russian authorities in 2014 for a murder a year prior in Moscow - a killing that bore hallmarks similar to the Berlin assassination.
Afterward, Western nations banded together to expel more than 100 Russian diplomats they accused of being spies, including 60 from the U.S.