"These are absolutely illegal, absolutely provocative and absolutely unfriendly actions of those who seek to hamper restoration of normal relations".
Earlier, Russia's envoy to Washington, Mr Anatoly Antonov, said he had sent a "decisive protest" to the USA over the removed flags.
In an interview on state television, Russia's new Ambassador to the United States Anatoly Antonov called the taking down of the flags "upsetting".
On September 2, the United States authorities shut down the Russian trade mission in Washington, DC and its branch in New York City.
In December 2016, two Russian diplomatic properties in NY and Maryland used by Russian diplomats were closed by the Obama administration over accusations of alleged Russian hacking during the presidential election.
Zakharova also said that in accordance with an instruction given by President Vladimir Putin, the Russian Foreign Ministry was in the process of selecting a legal firm to start a court proceeding over the seizure of diplomatic properties.
Russia vehemently opposes the USA move to take down Russian flags from its ceased diplomatic properties in San Francisco, the Russian embassy in Washington, DC said in a statement on Wednesday. "Of course, the Russian Federation has not given any consent for the flags to be removed", Zakharova said.
"We demand an immediate end to the takeover of our property in the USA, which is accompanied by offensive actions", Mr Antonov added. "We demand the U.S.immediately returns the Russian state symbols to their place and prevents such incidents in the future", the embassy said in a statement.
In late August, the United States ordered Russian Federation to close its consulate in San Francisco and two other installations as relations between the two former Cold War enemies took another dive.
"The flags at the former Russian consular properties in San Francisco were respectfully lowered and are safely stored within each of the buildings", the official said on Wednesday.