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Federal agents in the United States carried out an inspection of a Russian trade mission in Washington on Saturday, amid escalating tensions between the two nations.
The visit comes two days after the US announced it was shuttering the Russian consulate in San Francisco as well as annexes in New York and Washington.
A report in Foreign Policy magazine claimed that Russian officials were forewarned of the inspection and had lit a fire to burn documents.
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Read more: Russia lashes out after Trump orders diplomatic posts closed
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Black smoke was seen billowing from the consulate in San Francisco on Friday.
A spokeswoman for the Russian foreign ministry insisted the smoke was due to measures to "preserve the building" at a time when officials were gearing up to leave.
US agents were seen in the gardens of the mansion in Washington as Russian news agency RIA-Novosti reported that the search was conducted with Russian officials present.
"Today, Russian Embassy personnel, together with State Department officials, walked through three properties in San Francisco, New York and Washington, DC that the Russian government is required to close," a State Department official said.
"These inspections were carried out to secure and protect the facilities and to confirm the Russian government had vacated the premises," he said, adding that all three are now closed.
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Read more: US orders Russia to close consulate but seeks 'to improve relations'
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The shuttering of the three properties by the Trump administration was in response to staff cuts enforced by Russia at the US mission in Moscow.
Russia’s foreign ministry is said to be furious with the inspection and presented acting US mission head Anthony Godfrey with a "note of protest over the intention of the American authorities to conduct a search."
The ministry warned that the visit "could be used by the US intelligence services to organise an anti-Russian provocation involving planting compromising materials."
"The US authorities must stop the gross violations of international law and breaching the immunity of Russia's diplomatic institutions. Otherwise, we reserve the right to reciprocate on mutual basis," the note added.
Tensions between the US and Russia have been rising over the past few months, despite Mr Trump vowing to improve relations with its former Cold War rival during his presidential campaign.