Although the managerial affairs department said that it had not employed the man, presidential spokesman Dmitry Peskov told journalists on Tuesday that Mr Smolenkov had worked in the presidential administration before he was "fired by an internal order a few years ago".
US Secretary of State Mike Pompeo on Tuesday angrily denounced news reports detailing the secret exfiltration of a Central Intelligence Agency mole who had operated at the top levels of the Kremlin, saying such reports could put lives at risk.
White House press secretary Stephanie Grisham blasted the network for the claim.
Details within CNN's story seemed to downplay Trump's role in the decision to extract the spy.
Media captionWhy did Trump give information to the Russians in the White House?
Instead, Mr. Brennan sent separate intelligence reports, many based on the source's information, in special sealed envelopes to the Oval Office.
The New York Times reports that some officials doubted his "trustworthiness" and had multiple "reasons to suspect the source could be a double agent", which "would nearly certainly mean that some of the information the informant provided about the Russian interference campaign or Mr. Putin's intentions would have been inaccurate". Those concerns were described to CNN by five sources who served in the Trump administration, intelligence agencies and Congress.
Russian media quickly came up with the name of Oleg Smolenkov.
Since then he has not been heard from, but real estate records show that an Oleg and Antonina Smolenkov purchased a house in Stafford, Virginia, about 40 miles (65 kilometers) south of the United States capital June 5, 2018. The reporter was tracked by two men in an SUV when he rang the doorbell, NBC said. It said Mr. Putin was, in part, motivated by a "grudge" against Democratic presidential candidate Hillary Clinton "for comments he nearly certainly saw as disparaging him".
"All these speculations in the American media that somebody urgently extracted someone and who rescued someone and so on are some sort of pulp fiction, you know".
Russian Foreign Minister Sergei Lavrov said on Tuesday he had never heard of Mr Smolenkov.
It sounds like the makings of a John le Carré espionage novel.
U.S. media, citing intelligence sources, said the CIA's Kremlin informant was crucial to the United States intelligence conclusion in late 2016 that Russian Federation was actively interfering in the USA election in Trump's favor.
If multiple media reports are to be believed, however, this is real life - and the USA political consequences could be significant.
Both CNN and the Times raise concerns about President Trump's treatment of highly classified information. It reflects a conclusion that an undisciplined commander-in-chief could pose a national security risk - even if only inadvertently.
In the first months of his administration, Trump's handling of classified intelligence further concerned intelligence officials. The president, who has spent much of his time feuding with, and occasionally directly condemning, the USA intelligence community - the so-called "deep state" - surely will be furious.