WASHINGTON — Soon after he took over as C.I.A. director, Mike Pompeo privately told lawmakers about a new target for American spies: Julian Assange, the founder of WikiLeaks.

Intent on finding out more about Mr. Assange’s dealings with Russian intelligence, the C.I.A. began last year to conduct traditional espionage against the organization, according to American officials. At the same time, federal law enforcement officials were reconsidering Mr. Assange’s designation as a journalist and debating whether to charge him with a crime.

Mr. Pompeo and former Attorney General Jeff Sessions unleashed an aggressive campaign against Mr. Assange, reversing an Obama-era view of WikiLeaks as a journalistic entity. For more than a year, the nation’s spies and investigators sought to learn about Mr. Assange and his ties to Russia as senior administration officials came to believe he was in league with Moscow.

Their work culminated in prosecutors secretly filing charges this summer against Mr. Assange, which were inadvertently revealed in an unrelated court filing and confirmed on Friday by a person familiar with the inquiry. Taken together, the C.I.A. spying and the Justice Department’s targeting of Mr. Assange represented a remarkable shift by both the American government and President Trump, who repeatedly lauded WikiLeaks during the 2016 campaign for its releases of Democratic emails, stolen by Russian agents, that damaged his opponent, Hillary Clinton.

Justice Department officials did not disclose the charges against Mr. Assange on Friday, prompting speculation around Washington about their nature. The case might be tied to the hacked Democratic emails, which are part of Mr. Mueller’s evidence of the wide-ranging election interference personally ordered by President Vladimir V. Putin of Russia. The charges could also be related to WikiLeaks’s publication last year of C.I.A. tools to penetrate computers and mobile devices, the so-called Vault 7 disclosures.

National security officials have long viewed Mr. Assange with hostility and considered him a threat. “He was a loathed figure inside the government,” said Andrea Kendall-Taylor, who served as a deputy national intelligence officer for Russia under the director of national intelligence until May.

This account is drawn from current and former officials familiar with the government’s effort to step up scrutiny of Mr. Assange.

American law enforcement officials began seriously investigating the ties between WikiLeaks and Russia after Edward Snowden, the former National Security Agency contractor who revealed closely held intelligence secrets, escaped to Russia in June 2013. Sarah Harrison, a WikiLeaks editor and one of Mr. Assange’s close advisers, accompanied Mr. Snowden to Moscow. Law enforcement officials wanted to know what role the group played in brokering Mr. Snowden’s asylum in Russia.

A year later, F.B.I. and C.I.A. officials began arguing internally that Mr. Assange was an information broker, not a journalist, former officials said. At one point, they pushed for a meeting with President Barack Obama to make the case that he was not a journalist, according to people briefed on the talks. The meeting never occurred.

Inside the Justice Department under Mr. Obama, some officials expressed reluctance to pursue Mr. Assange because he could be construed as part of the news media. Obama administration officials were hesitant to wage a high-profile fight with Mr. Assange after being criticized heavily by the news media for obtaining records of journalists through court subpoenas in pursuit of leakers. The step is considered an intrusion on press freedoms.

Mr. Assange seemed to have crossed into uncharted ground by 2016 with the publication of emails stolen from the Democratic National Committee’s servers and Mrs. Clinton’s campaign chairman, former F.B.I. officials said. He was deliberately attacking Mrs. Clinton over Mr. Trump and coordinating with Russian intelligence operatives, wittingly or not, to maximize the damage to her campaign.

Mr. Pompeo, then a Republican congressman from Kansas, initially praised the WikiLeaks disclosures. But once he took over the C.I.A., his rhetoric hardened.

His first speech as director came a month after WikiLeaks published the archive of hacking tools stolen from the C.I.A., seriously eroding the agency’s ability to conduct electronic espionage.

Mr. Pompeo laid down a gauntlet. “WikiLeaks walks like a hostile intelligence service and talks like a hostile intelligence service,” he said last April.

To support his assessment, Mr. Pompeo cited how the group had encouraged followers to join the C.I.A. and steal secrets, and how “it overwhelmingly focuses on the United States while seeking support from anti-democratic countries.”

After his speech, Mr. Pompeo headed to Congress to privately brief members conducting intelligence oversight on the C.I.A. efforts against WikiLeaks. Mr. Pompeo said the agency was conducting counterintelligence collection, which can include developing informants and penetrating computers overseas, officials said.

Mr. Pompeo also seemed to hold open the possibility that the intelligence community could begin other, more aggressive efforts to try to disrupt WikiLeaks. Some lawmakers expressed discomfort, according to an American official.

The speech by Mr. Pompeo, who has since become secretary of state, and other efforts were intended in part to pressure the Justice Department to intensify its reassessment of Mr. Assange, an intelligence official said.

Law enforcement officials had been trying to learn more about Mr. Assange’s knowledge of WikiLeaks’s interactions with Russian intelligence officers and its other actions, and for a time seemed willing to offer him some form of immunity from prosecutions in exchange for his testimony, reaching out to his lawyers. But Mr. Assange’s release of the Vault 7 tools ended those negotiations.

Senior Justice Department officials pushed in 2017 to declare internally that WikiLeaks was not covered by special rules governing how investigators interact with journalists. The regulations require higher-level approval to obtain journalists’ records, like phone logs and emails, as part of investigations into leaks of classified information. By releasing hacking tools and playing a role in disrupting the election, Mr. Assange, the senior officials argued, was acting more like an agent of a foreign power than a journalist.

Mr. Assange may have begun working with Russian intelligence without knowing with whom he dealt, said Ms. Kendall-Taylor, now a senior fellow with the Center for a New American Security. The intermediaries and cutouts sent by Russian intelligence to deal with Mr. Assange were supposed to give him plausible deniability.

“But as he spent more time, the relationship with the Russians grew closer,” she said. “I would expect that he knows what he is doing by the end of this.”

Federal prosecutors began working on a sealed criminal complaint this summer, a former law enforcement official said. It was not clear whether the Justice Department declared that Mr. Assange was not a journalist or whether prosecutors gathered sufficient evidence to charge him without resolving that issue.

Mr. Assange’s case also has implications for Mr. Mueller.

In July, the special counsel charged 12 Russian military intelligence operatives with interfering in the 2016 election. That indictment contained thinly veiled references to WikiLeaks, identifying it as “Organization 1.” Notably, the indictment did not identify the organization as a member of the news media, and it asserted that the Russian operatives transferred their stolen documents to WikiLeaks.

WikiLeaks encouraged “Guccifer 2.0,” the online persona of the Russian operatives, to provide it with the Democratic documents because it would “have a much higher impact,” according to court papers.

Whether anyone connected with the Trump campaign worked with Mr. Assange or others to carry out Russia’s scheme to interfere in the 2016 presidential race is at the heart of Mr. Mueller’s inquiry.

So far, no evidence has publicly emerged that anyone in the Trump campaign conspired with Moscow’s disruption, and Mr. Trump has repeatedly denied any “collusion” with Russia. But the special counsel’s office continues to summon witnesses before a federal grand jury, asking about interactions between allies of Mr. Trump and Mr. Assange through intermediaries or other means.

What has become abundantly clear since the election is that various associates of Mr. Trump’s tried their best to figure out what information Mr. Assange possessed, how it might harm the Clinton campaign and when he planned to release it.

About a month before the election, for instance, Donald Trump Jr., a key adviser to his father, sent WikiLeaks a private message on Twitter asking about speculation that Mr. Assange planned to soon release documents that would prove devastating to Mrs. Clinton. “What’s behind this Wed leak I keep reading about?” he asked. He has said he got no response and never corresponded with WikiLeaks again.

Charges against Mr. Assange would be a big step, said Joshua Geltzer, a former official in the Justice Department’s national security division. But, he added, the precise nature of the charges may not be known until Mr. Assange is in the custody of American officials. Mr. Assange has lived in the Ecuadorean Embassy in London since 2012, forced there as he sought refuge from Swedish prosecutors who pursued him on charges of sexual abuse.

“The government has certainly been concerned about and looking at Assange for a long time,” Mr. Geltzer said. “Ultimately, the stakes are high in this one, given the complexities of the case, and the government must be prepared for that going in.”