The disclosure to the Russians by the President, though not about the Russian spy specifically, prompted intelligence officials to renew earlier discussions about the potential risk of exposure, according to the source directly involved in the matter.
At the time, then-CIA Director Mike Pompeo told other senior Trump administration officials that too much information was coming out regarding the covert source, known as an asset. An extraction, or "exfiltration" as such an operation is referred to by intelligence officials, is an extraordinary remedy when US intelligence believes an asset is in immediate danger.
The source was considered the highest level source for the US inside the Kremlin, high up in the national security infrastructure, according to the source familiar with the matter and a former senior intelligence official.
According to CNN's sources, the spy had access to Putin and could even provide images of documents on the Russian leader's desk.
The covert source provided information for more than a decade, according to the sources, and an initial effort to extract the spy, after exposure concerns, was rebuffed by the informant.
CNN is reporting the additional information about the covert source who was extracted from Russia in 2017. The information, which adds further understanding to the value of the informant, was initially withheld by CNN but was subsequently reported by the New York Times Monday evening.
A US official said before the secret operation there was media speculation about the existence of such a covert source, and such coverage or public speculation poses risks to the safety of anyone a foreign government suspects may be involved. This official did not identify any public reporting to that effect at the time of this decision and CNN could not find any related reference in media reports.
Asked for comment, Brittany Bramell, the CIA director of public affairs, told CNN: "CNN's narrative that the Central Intelligence Agency makes life-or-death decisions based on anything other than objective analysis and sound collection is simply false. Misguided speculation that the President's handling of our nation's most sensitive intelligencewhich he has access to each and every daydrove an alleged exfiltration operation is inaccurate."
A spokesperson for Secretary of State Mike Pompeo declined to comment. White House press secretary Stephanie Grisham said, "CNN's reporting is not only incorrect, it has the potential to put lives in danger."
The removal happened at a time of wide concern in the intelligence community about mishandling of intelligence by Trump and his administration. Those concerns were described to CNN by five sources who served in the Trump administration, intelligence agencies and Congress.
Those concerns continued to grow in the period after Trump's Oval Office meeting with Kislyak and Lavrov. Weeks after the decision to extract the spy, in July 2017, Trump met privately with Russian President Vladimir Putin at the G20 summit in Hamburg and took the unusual step of confiscating the interpreter's notes. Afterward, intelligence officials again expressed concern that the President may have improperly discussed classified intelligence with Russia, according to an intelligence source with knowledge of the intelligence community's response to the Trump-Putin meeting.
Knowledge of the Russian covert source's existence was highly restricted within the US government and intelligence agencies. According to one source, there was "no equal alternative" inside the Russian government, providing both insight and information on Putin.
"The impact would be huge because it is so hard to develop sources like that in any denied area, particularly Russia, because the surveillance and security there is so stringent," a former senior intelligence official told CNN. "You can't reacquire a capability like that overnight."
The decision to pull the asset out of Russia was the culmination of months of mounting fear within the intelligence community.
At the end of the Obama administration, US intelligence officials had already expressed concerns about the safety of this spy and other Russian assets, given the length of their cooperation with the US, according to the former senior intelligence official.
In the first months of his administration, Trump's handling of classified intelligence further concerned intelligence officials. Ultimately, they decided to launch the difficult operation to remove an asset who had been working for the US for years.
The President was informed in advance of the extraction, along with a small number of senior officials. Details of the extraction itself remain secret and the whereabouts of the asset today are unknown to CNN.
UPDATE: This story has been updated to include additional details about the covert source.
CNN's Marshall Cohen contributed to this report.