Russia "carries out counterintelligence activities against those who are suspected of espionage," Peskov said. "This is done regularly."
He spoke after British Foreign Secretary Jeremy Hunt warned Friday that Whelan, who also holds British, Irish and Canadian passports, should not be used as a pawn in "diplomatic chess games".
Analysts have speculated that Whelan, 48, was arrested to pave the way for a possible spy swap with a Russian agent arrested abroad, possibly Marina Butina, a gun rights campaigner who was convicted of being a "foreign agent" in the United States last month.
The New York Times has reported that the Marine Corps court-martialed Whelan in 2008 on charges of larceny and passing bad checks, an offence that in most cases disqualifies candidates from foreign intelligence work.
Whelan's Russian lawyer Vladimir Zherebenkov said his client had been charged with espionage, although deputy foreign minister Sergei Ryabkov later said Whelan has not yet been formally charged. Espionage is punishable by up to 20 years in jail.
The British, Canadian and Irish embassies have also been granted consular access to Whelan, his family said Tuesday.
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