The Investigation Committee at the General Prosecutor's Office "initiated a genocide probe based on reports of actions committed by Georgian troops aimed at murdering Russian citizens - ethnic Ossetians - living in South Ossetia," said Igor Komissarov, deputy chairman of the Investigation Committee.
Russia has accused Georgia of committing "genocide" by launching an offensive last Friday to regain control of the separatist province of South Ossetia. Russia is calling for an international war crimes trial for the Georgian leadership, which Moscow says is responsible for massive loss of life in South Ossetia.
President Dmitry Medvedev ordered prosecutors on August 10 to gather evidence to support Russian allegations of the Georgian genocide of South Ossetians. The vast majority of South Ossetians hold Russian passports.
Russia has said that 1,600 civilians died in the Georgian attack on Tskhinvali, the capital of the breakaway republic of South Ossetia.
Georgia has also filed a lawsuit against Russia at the International Court of Justice on Tuesday over alleged ethnic cleansing.
"The suit contains material showing that Russia has committed ethnic cleansing against Georgia [during three interventions in South Ossetia and Abkhazia] from 1993 to 2008," Georgian National Security Council Secretary Alexander Lomaya said.
Speaking on South Ossetia's events earlier this week, the Russian prime minister accused the West of double standards.
"They [the U.S.] of course had to hang Saddam Hussein for destroying several Shiite villages," Vladimir Putin said.
"But the current Georgian rulers, who in one hour simply wiped ten Ossetian villages from the face of the earth, who used tanks to knock down children and the elderly, and who burnt civilians alive - they (Georgian leaders) are players who of course have to be protected."