US President Joe Biden and Russia's Vladimir Putin met in Geneva last week (Representational).
Russian state prosecutor's office said on Monday it banned Bard College, a US non-governmental organisation, after labelling it "undesirable".
The Russian foreign ministry said in April it would end the activity in Russia of US funds and NGOs which it believed interfere in the country's internal affairs, in retaliation to an array of US government sanctions imposed on Moscow.
The state prosecutor's office said that the activity of educational NGO Bard College "represents the threat to the constitutional order and security of Russian Federation".
Bard was not immediately available to comment.
Russia-US ties slumped to a new post-Cold War in March after US President Joe Biden said he thought his Russian counterpart Vladimir Putin was a "killer", while Moscow and Washington recalled their ambassadors.
Biden and Putin met in Geneva last week and agreed for the envoys to return.
Speaking at a news conference after meeting with Biden, Putin said the organizations, which are supported by the United States, would "contain" Russia.
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