The United States in August ordered Russia to close its San Francisco consulate and two other installations.
"Yesterday we learned about a new hostile act of the US authorities against our diplomatic missions," foreign ministry spokeswoman Maria Zakharova told reporters.
"We've already lodged a decisive protest with the United States."
She complained that Russian flags had been "torn down" from the buildings of the general consulate in San Francisco and Russia's trade mission in Washington.
The United States in August ordered Russia to close its San Francisco consulate and two other installations as relations between the two former Cold War enemies took another nose-dive.
"Obviously the Russian side has never agreed to its flags being removed," Zakharova said, calling the removal "a violation of a Russian state symbol."
"The Russian side will decide on retaliatory measures," Zakharova added.
Also on Thursday, the Russian parliament's lower house, the Duma, cancelled a visit to the US by a group of lawmakers planned for this month, a Duma spokeswoman told AFP.
Russia's ambassador to Washington Anatoly Antonov also denounced the move.
"Such steps only complicate US-Russian dialogue," Antonov said in televised remarks.
"We demand an immediate end to the takeover of our property in the US which is accompanied by offensive actions," he added.
The latest flare-up comes as Jon Huntsman, Washington's new ambassador to Moscow, is preparing to assume his role.
Zakharova warned that the removal of the flags could complicate the beginning of Huntsman's tenure.
Washington ordered the shutdown of the Russian diplomatic missions after the Kremlin demanded that the US slash staff numbers at its missions in Russia.
Moscow also accused the United States of searching its missions, including accommodations for diplomatic staff.
The dispute is the latest twist in tortured ties between the US and Russia, which have slumped to their lowest point since the Cold War following the Kremlin's seizure of Crimea from Ukraine in 2014.
The West imposed punishing sanctions on Russia over its meddling in its ex-Soviet neighbour, sparking a revenge embargo from Moscow against agricultural products.
US President Donald Trump initially pledged to improve ties, but those promises have been overshadowed by allegations of collusion between Russia and members of Trump's election campaign.