The council's plaque has been removed from the British Consulate General office, which accommodated the British government's cultural arm in the Urals city. There are no notices on the building, and the office is not answering phone calls, a RIA Novosti correspondent reported.
The cultural organization's offices in St. Petersburg and Yekaterinburg resumed work after the New Year holidays despite Russia's order they be closed from the start of this year, a move Moscow called a provocation.
The Russian government has accused the council of irregularities in its legal status and non-payment of taxes, charges that London denies.
A notice on the building of the British Council's office in St. Petersburg says the organization has suspended work "over Russian authorities' actions," but will resume activities soon.
Russian employees of the St. Petersburg and Yekaterinburg offices were summoned for "interviews" with Russian security officials on Wednesday, and on Tuesday evening the head of the St. Petersburg office, Stephen Kinnock, was briefly detained by police.
The U.K. Foreign Office warned the Russian government against any attempts to intimidate British Council staff.
Russia's main domestic security body, the Federal Security Service, earlier said the interviews were designed to "save Russian staff from any possible provocations."
The dispute is the latest blow to relations between the two countries, already strained over the murder of former Russian security officer Alexander Litvinenko in London in 2006.
Observers have called the claims against the British Council politically motivated. Moscow has insisted its demands are legitimate and urged greater respect for national laws.
A spokesman for the St. Petersburg office told RIA Novosti, citing Kinnock, that the British Council would make a formal statement on the situation from London on Thursday.
The BBC quoted diplomatic sources on Thursday as saying the Foreign Office does not seem to have "much appetite for retaliation" against Moscow as it recognizes that "Britain has few options left in the row."