Russian Federal Migration Service (FMS) said almost 300 migrants from the impoverished Central Asian state were detained over the last several days for violations of Russian law and would now be deported.
The move comes after a court in Tajikistan this week jailed two pilots from Russia and Estonia for eight-and-a-half years on charges of smuggling contraband goods, a verdict that was angrily protested by Moscow.
The Interfax news agency quoted a source at the FMS as saying the crackdown on illegal migrants would continue at the weekend. Its spokeswoman Zalina Kornilova said 297 Tajik migrants had already been detained.
"The 297 citizens of Tajikistan, who according to the court's decision are going to be deported from the Russian Federation, are in temporary holding centres. Just technical questions need to be solved," she told Interfax.
The FMS denied that the crackdown was politically motivated but a foreign ministry source told the Kommersant daily that the deportations were part of an "asymmetric response" by Moscow in protest against the pilot's jailing.
Rights activists complained that while Moscow needed to defend the rights of Russian pilot Vladimir Sadovnichy, mass deportations of economic migrants was an unjust measure.
"If this is Russia's reaction to the pilots' jailing then it's ridiculous," said veteran rights activist Svetlana Gannushkina who runs a support group for migrants.
"They are preparing to deport from our country innocent people who round the clock have been working to build the city," she told Kommersant.
Tajikistan is the poorest country to emerge after the collapse of the Soviet Union with a per capita Gross National Income of just $800, according to the World Bank.
This has prompted massive migration especially to Moscow, where tens of thousands of Tajiks work on building sites and in communal services. Their remittances home provide crucial income for the Tajik economy.
According to the FMS, there are 700,000 Tajiks living officially in Russia, a tenth of the country's population of just under 7 million.