WASHINGTON—Decades ago, the CIA recruited and carefully cultivated a midlevel Russian official who began rapidly advancing through the governmental ranks. Eventually, American spies struck gold: The longtime source landed an influential position that came with access to the highest level of the Kremlin.

As U.S. officials began to realize that Russia was trying to sabotage the 2016 presidential election, the informant became one of the CIA’s most important — and highly protected — assets. But when intelligence officials revealed the severity of Russia’s election interference with unusual detail later that year, the news media picked up on details about the CIA’s Kremlin sources.

CIA officials worried about safety made the arduous decision in late 2016 to offer to extract the source from Russia. The situation grew more tense when the informant at first refused, citing family concerns — prompting consternation at CIA headquarters and sowing doubts among some U.S. counterintelligence officials about the informant’s trustworthiness. But the CIA pressed again months later after more media inquiries. This time, the informant agreed.

The move brought to an end the career of one of the CIA’s most important sources. It also effectively blinded U.S. intelligence officials to the view from inside Russia as they sought clues about Kremlin interference in the 2018 midterm elections and next year’s presidential contest.

CNN first reported the 2017 extraction on Monday. Other details — including the source’s history with the agency, the initial 2016 exfiltration offer and the cascade of doubts set off by the informant’s subsequent refusal — have not been previously reported. This article is based on interviews in recent months with current and former officials who spoke on the condition that their names not be used discussing classified information.

Officials did not disclose the informant’s identity or new location, both closely held secrets. The person’s life remains in danger, current and former officials said, pointing to Moscow’s attempts last year to assassinate Sergei V. Skripal, a former Russian intelligence official who moved to Britain as part of a high-profile spy exchange in 2010.

The Moscow informant was instrumental to the CIA’s most explosive conclusion about Russia’s interference campaign: that President Vladimir Putin ordered and orchestrated it himself. As the U.S. government’s best insight into the thinking of and orders from Putin, the source was also key to the CIA’s assessment that he affirmatively favoured Donald Trump’s election and personally ordered the hacking of the Democratic National Committee.

The informant, according to people familiar with the matter, was outside Putin’s inner circle, but saw him regularly and had access to high-level Kremlin decision-making — easily making the source one of the agency’s most valuable assets.

Handling and running a Moscow-based informant is extremely difficult because of Putin’s counterintelligence defences. The Russians are known to make life miserable for foreign spies, following them constantly and at times roughing them up. Former CIA employees describe the entanglements as “Moscow rules.”

The informant’s information was so delicate, and the need to protect the source’s identity so important, that the CIA director at the time, John O. Brennan, kept information from the operative out of President Barack Obama’s daily brief in 2016. Instead, Brennan sent separate intelligence reports, many based on the source’s information, in special sealed envelopes to the Oval Office.

The information itself was so important and potentially contentious in 2016 that top CIA officials ordered a full review of the informant’s record, according to people briefed on the matter. Officials reviewed information the source had provided years earlier to ensure that it had proved accurate.

Even though the review passed muster, the source’s rejection of the CIA’s initial offer of exfiltration prompted doubts among some counterintelligence officials. They wondered whether the informant had been turned and had become a double agent, secretly betraying his American handlers. That would almost certainly mean that some of the information the informant provided about the Russian interference campaign or Putin’s intentions would have been inaccurate.

Some operatives had other reasons to suspect the source could be a double agent, according to two former officials, but they declined to explain further.

Other current and former officials who acknowledged the doubts said they were put to rest when the source agreed to be extracted after the CIA asked a second time.

Leaving behind one’s native country is a weighty decision, said Joseph Augustyn, a former senior CIA officer who once ran the agency’s defector resettlement centre. Often, informants have kept their spy work secret from their families.

“It’s a very difficult decision to make, but it is their decision to make,” Augustyn said. “There have been times when people have not come out when we strongly suggested that they should.”

The decision to extract the informant was driven “in part” because of concerns that Trump and his administration had mishandled delicate intelligence, CNN reported. But former intelligence officials said there was no public evidence that Trump directly endangered the source, and other current U.S. officials insisted that media scrutiny of the agency’s sources alone was the impetus for the extraction.

Trump was first briefed on the intelligence about Russian interference, including material from the prized informant, two weeks before his inauguration. A CIA spokeswoman responding to the CNN report called the assertion that Trump’s handling of intelligence drove the reported extraction “misguided speculation.”

Some former intelligence officials said the president’s closed-door meetings with Putin and other Russian officials, along with Twitter posts about delicate intelligence matters, have sown concern among overseas sources.

“We have a president who, unlike any other president in modern history, is willing to use sensitive, classified intelligence however he sees fit,” said Steven L. Hall, a former CIA official who led the agency’s Russia operations. “He does it in front of our adversaries. He does it by tweet. We are in uncharted waters.”

But the government had indicated that the source existed long before Trump took office, first in formally accusing Russia of interference in October 2016 and then when intelligence officials declassified parts of their assessment about the interference campaign for public release in January 2017. News agencies, including NBC, began reporting around that time about Putin’s involvement in the election sabotage and on the CIA’s possible sources for the assessment.

The following month, The Washington Post reported that the CIA’s conclusions relied on “sourcing deep inside the Russian government.” And The New York Times later published articles disclosing details about the source.

The news reporting in the spring and summer of 2017 convinced U.S. government officials that they had to update and revive their extraction plan, according to people familiar the matter.

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The extraction ensured the informant was in a safer position and rewarded for a long career in service to the United States. But it came at a great cost: It left the CIA struggling to understand what was going on inside the highest ranks of the Kremlin.

The agency has long struggled to recruit sources close to Putin, a former intelligence officer himself wary of CIA operations. He confides in only a small group of people and has rigorous operational security, eschewing electronic communications.

James R. Clapper Jr., the former director of national intelligence who left office at the end of the Obama administration, said he had no knowledge of the decision to conduct an extraction. But, he said, there was little doubt that revelations about the extraction are “going to make recruiting assets in Russia even more difficult than it already is.”

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