If true, it would amount to one of the West's biggest intelligence coups since the end of the Cold War.
The newspaper, Kommersant, named the man as Colonel Shcherbakov, and said he was responsible for unmasking a Russian spy ring in the United States in June, involving London-based Anna Chapman, 28. Their arrests humiliated Moscow and strained diplomatic links.
The betrayal would make Shcherbakov one of the most senior traitors since the fall of the Soviet Union and could have consequences for Russia's Foreign Intelligence Service (SVR) and its chief, former prime minister Mikhail Fradkov.
The newspaper said Shcherbakov - whose first name it did not give - had been responsible for "illegal spying" in the US, meaning spies operating under deep cover without diplomatic immunity. "There has never been such a failure by Section S, the American department that Shcherbakov directed," said Gennady Gudkov, deputy chairman of the Russian parliament's security committee.
Shcherbakov had left Russia days before US authorities announced the spy-ring arrests on 28 June - and a Kremlin official was quoted as saying a Russian hit squad was probably already planning to kill him.
"We know who he is and where he is," the unidentified official said. "Do not doubt that a Mercader has been sent after him already."
Ramon Mercader was the Russian agent who murdered exiled Bolshevik Leon Trotsky with an ice axe near Mexico City in 1940 on Joseph Stalin's orders. All the ten spies arrested in the US pleaded guilty and were deported to Russia in a spy swap less than two weeks later.
Prime minister Vladimir Putin, himself a former KGB spy, greeted them as heroes. He said traitors came to a bad end, and that the informer would be left to the mercy of his own kind.
"The special services live by their own laws and everyone knows what these laws are," he said. Despite Moscow's tough talk, the revelation could damage the reputation of the SVR.
Kommersant cited an unidentified source as saying that Mr Fradkov could be sacked and the SVR folded into the powerful Federal Security Service (FSB), successor of the Soviet-era KGB.
"The damage inflicted by Shcherbakov is so enormous that a special commission should be created to analyse the reasons which allowed this complete failure to happen," Mr Gudkov said. "And then we should decide what should happen to the SVR and its unique Section S."
US authorities have previously said the Chapman spy ring had operated for at least a decade.