The BBC's Russian-language Service was taken off the FM frequency it had been using to broadcast to Moscow on Friday, the second such stoppage in nine months.
The BBC said in a statement the Russian FM radio station that had been re-broadcasting its Russian Service programmes had been told by licensing authorities to stop or risk being taken off the air itself.
The move comes two months after a round of diplomatic expulsions brought relations between London and Moscow to their lowest point in years.
Almost all of Russia's broadcast media is deferential in its coverage of the Kremlin. Critics of President Vladimir Putin say his officials have sidelined dissenting voices on radio and television, though he denies this.
BBC Russian Service programmes have since May been broadcast on Bolshoye Radio, which is owned by financial group Finam.
In a statement, the BBC said Finam had been told by the licensing authorities that Bolshoye Radio's licence barred it from airing material supplied by third parties. The BBC said this was not true.
"We are extremely disappointed that listeners to Bolshoye Radio in Moscow will be unable to listen to our impartial and independent news programming," said Richard Sambrook, director of BBC Global News.
He said the BBC will be appealing to the Russian licensing authorities. "We will ask for the decision to be reviewed and for the original concept of the station to be respected.