Mikhail Kamynin told journalists that Georgia's charge d'affaires had been summoned to the ministry and informed of the decision.
"The Georgian diplomat was told that the Russian Federation, in response to unfriendly actions from Georgia, had decided to declare three senior diplomats at the Georgian Embassy in Moscow personae non gratae," Kamynin said.
Before announcing the current 15-day state of emergency on Wednesday, Georgian President Mikheil Saakashvili blamed "high ranking officials in Russia's special services" for the recent unrest in the country, and said several Russian diplomats would be expelled from Georgia for spying.
Kamynin also said Georgia's accusations that Russia had stirred up unrest in Tbilisi are an attempt to hide the leadership's helplessness in dealing with their internal problems.
President Saakashvili said in a TV address to the nation on Wednesday that Russia's special services were behind recent events in Tbilisi, adding that Georgian special services had information that an alternative Georgian government had been formed in Russia.
"This is merely an attempt by the Georgian authorities to hide their helplessness in resolving their interior affairs," Kamynin said.
On Wednesday, after hundreds of riot police with shields and batons broke up a rally outside the Georgian parliament, opposition supporters staged a new protest on the city's Rike Square. The police again employed harsh methods to dispel the crowd, including rubber bullets and tear gas. The authorities said that 360 people were injured in the clashes. The protesters were demanding President Saakashvili's resignation and early elections.
Russia-Georgia relations were aggravated in the fall of 2006 after Georgian law enforcement agencies detained four Russian servicemen on suspicion of espionage on September 27. In October, Georgia handed the officers over to the Organization for Security and Cooperation in Europe.
Russia then recalled its ambassador in Tbilisi to Moscow for consultations and announced the evacuation of employees of Russian companies in Georgia. On January 22, 2007, the Russian ambassador returned to Tbilisi.