Russian schools were also ordered to compile lists of children with Georgian surnames to detect illegal immigrants.
The deportation, which was carried out by the Kremlin's emergency situations ministry, was the latest in a series of reprisals against Russia's sizeable Georgian community after four Russian soldiers in Georgia were arrested on suspicion of spying. The four were released on Monday.
In recent days police have raided Georgian restaurants and other businesses in Moscow, apparently looking for minor legal violations in order to force their closure or criminalise their owners.
Alexander Gavrilov, a spokesman for Moscow city hall's education department, said some city schools had been asked to draw up the lists of schoolchildren.
He criticised the police action, saying that all children, irrespective of nationality, had an equal right to education.
"If the law enforcement bodies carry out work searching for illegal migrants, it's their business and there is no way schools must be involved in this process," said Mr Gavrilov.
Moscow police denied asking for the lists, but the Kommersant newspaper quoted a high-ranking police official who confirmed the measures, claiming the interior ministry had instigated it. Georgians in Moscow claimed they were suffering collective punishment at the hands of the Russian authorities, comparing their plight to the persecution of minority groups such as Jews during the country's Soviet era.
"They're crushing people, they're destroying families. They used to persecute Jews like this. Now it's the Georgians' turn," said Inna Bashkirova, who joined a crowd of her compatriots in front of the Georgian consulate, many of who were trying to get home after Russia severed all transport links between the states.
"If (Georgian President Mikhail) Saakashvili did something wrong, why do common people suffer?" she asked.
The Kremlin imposed an economic embargo on Georgia following the crisis, which saw Moscow hint at military action against its pro-western neighbour.
Russia's lower house of parliament is also considering legislation to limit bank transfers to foreign countries, in what would be a blow to the 1 million Georgians in Russia. They send an estimated £1.1bn every year to relatives at home, about 20% of the impoverished country's GDP.
It was also announced that people with dual citizenship, who include many Georgians, would no longer be allowed to work for the state.
Relations between the two neighbours have long been strained over Georgia's bid to join Nato and claims that Russia was supporting two Georgian breakaway provinces - accusations denied in Moscow.
Mr Saakashvili accused Russia of responding with "hysteria" to the arrest of the soldiers, who were said to be spying on the Georgian military.
But Russia's president, Vladimir Putin, was in no mood for compromise. "I would not counsel anyone to talk to Russia in the language of provocation and blackmail," he said at a meeting with parliamentary leaders on Wednesday.
