Current and former officials said that the arrangement has been a source of apprehension among the CIA's upper ranks and that they could not recall a time in the agency's history when a director faced a comparable conflict.
"Pompeo is in a delicate situation unlike any other director has faced, certainly in my memory," said Rolf Mowatt-Larssen, a CIA official for 23 years who served in Russia and held high-level positions at headquarters, "because of his duty to protect and provide the truth to an independent investigation while maintaining his role with the president."
The Russia issue has complicated Pompeo's effort to manage a badly strained relationship between the agency and a president who has disparaged its work and compared U.S. intelligence officials to Nazis. Amid that tension, Pompeo's interactions with the counterintelligence center have come under particular scrutiny.
The unit helped trigger the investigation into possible collusion between the Trump campaign and Russia by serving as a conduit to the FBI last year for information the CIA developed on contacts between Russian individuals and Trump campaign associates, officials said.
The center works more closely with the FBI than almost any other CIA department does, officials said, and continues to pursue leads on Moscow's election interference operation that could factor in the probe led by special counsel Robert S. Mueller III, a former FBI director.
Pompeo has not impeded that work, officials said. But several officials said there is concern about what he might do if the CIA uncovered new information potentially damaging to Trump and Pompeo were forced to choose between protecting the agency or the president.
"People have to watch him," said a U.S. official who, like others, requested anonymity to speak frankly. "It's almost as if he can't resist the impulse to be political."
A second former CIA official cited a "real concern for interference and politicization," saying that the worry among some at the agency is "that if you were passing on something too dicey [to Pompeo] he would go to the White House with it."
Pompeo has attributed his direct supervision of the counterintelligence center to a desire to place a greater emphasis on preventing leaks and protecting classified secrets — core missions of the center that are also top priorities for Trump.
Having the center report to him was designed "to send a signal to the workforce that this was important and we weren't going to tolerate misbehavior," he said at a security conference in Aspen, Colo., last month.
CIA spokesman Ryan Trapani described the suggestion that Pompeo might abuse his position as "ridiculous."
Executive-order guidelines prohibit the CIA from passing information to the White House "for the purpose of affecting the political process in the United States," Trapani said. "The FBI and special counsel's office are leading the law enforcement investigation into this matter — not CIA. CIA is providing relevant information in support of that investigation, and neither the director nor CIA will interfere with it."
Pompeo, 53, arrived as director at the CIA just days after Trump delivered a self-aggrandizing post-inaugural speech at agency headquarters. Appearing before a wall of carved granite stars that commemorate CIA officers killed in the line of duty, Trump used the occasion to browbeat the media and make false claims about the size of his inauguration crowds.
Pompeo has worked to overcome that inauspicious start, winning over many in the CIA workforce with his vocal support for aggressive intelligence gathering, his command of complex global issues and his influence at the White House. Pompeo spends several hours there almost every day, according to officials who said he has developed a strong rapport with the president.
But Pompeo is also known for berating subordinates, aggressively challenging agency analysts and displaying the fierce partisanship that became his signature while serving as a GOP member of Congress.
When asked about Russian election interference, Pompeo often becomes testy and recites talking points that seem designed to appease a president who rejects the allegations as "fake news" conjured by Democrats to delegitimize his election win.
"It is true" that Russia interfered in the 2016 election, Pompeo said at Aspen, "and the one before that, and the one before that . . . "
The phrasing, which Pompeo has repeated in other settings, casts last year's events as an unremarkable continuation of a long-standing pattern, rather than the unprecedented Kremlin operation described in a consensus report that the CIA and other agencies released in January.
Russia's intervention in 2016 represented "a significant escalation in directness, level of activity, and scope of effort," the report concluded. Its goal went beyond seeking to discredit U.S. democratic processes, the report said, and in the end was aimed at trying "to help President-elect Trump's election chances."
Pompeo has taken more hawkish positions on other areas of tension with Russia, saying that Moscow intervened in Syria, for example, in part because "they love to stick it to America."
Almost all CIA directors have had to find ways to manage a supposedly apolitical spy agency while meeting the demands of a president. But Trump, who has fired his FBI chief and lashed out at his attorney general over the Russia probe, appears to expect a particularly personal brand of loyalty.
"It is always a balancing act between a director's access to the president and the need to protect CIA's sensitive equities," said John Sipher, a former senior CIA official who also served in Russia. "Pompeo clearly has a more difficult challenge in maintaining that balance than his predecessors given the obvious concerns with this president's unique personality, obsession with charges against him, lack of knowledge and tendency to take impulsive action."
Pompeo has shown a willingness to handle political assignments for the White House. Earlier this year, he and other officials were enlisted to make calls to news organizations — speaking on the condition of anonymity — to dispute a New York Times article about contacts between Russians and individuals tied to the Trump campaign. Pompeo has never publicly acknowledged his involvement in that effort.
He has also declined to address whether he was approached by Trump earlier this year — as other top intelligence officials were — to publicly deny the existence of any evidence of collusion with Russia or to intervene with then-FBI Director James B. Comey to urge the FBI to back off its investigation of former national security adviser Michael Flynn.
Pompeo has, by all accounts, a closer relationship with Trump than others who did field such requests, including Director of National Intelligence Daniel Coats and National Security Agency Director Mike Rogers.
Pompeo was exposed to Trump's wrath over the Russia investigation on at least one occasion, officials said. He was among those present for a meeting at the White House earlier this year when Trump began complaining about the probe and, in front of Pompeo and others, asked what could be done about it.
Trapani, the CIA spokesman, declined to address the matter or say whether Pompeo has been questioned about it by Mueller. Pompeo's conversations with Trump "are entitled to confidentiality," Trapani said, adding that "the director has never been asked by the president to do anything inappropriate."
Pompeo spends more time at the White House than his recent CIA predecessors and is seen as more willing to engage in policy battles. In interviews and public appearances, Pompeo has advocated ousting the totalitarian regime in North Korea, accused the Obama administration of "inviting" Russia into Syria and criticized the nuclear accord with Iran.
Pompeo has also come under scrutiny on social issues. As part of an effort to expand chaplain services to CIA employees — which Trapani said was in response to requests from the agency workforce — Pompeo has consulted with Tony Perkins, president of the Family Research Council, an organization that the Southern Poverty Law Center has labeled an anti-gay hate group. Perkins has described that characterization as "reckless."
When Trump came under criticism for failing to specifically condemn Nazi sympathizers taking part in protests in Charlottesville — instead lamenting violence by "many sides" — Pompeo defended the president in a CBS interview, saying that Trump's condemnation of bigotry was "frankly pretty unambiguous."
Pompeo inherited an agency that had undergone a major reorganization under his predecessor, combing analysts and operators in a constellation of "centers" responsible for geographic regions, as well as transnational issues such as terrorism.
Pompeo's alterations have been minimal. He added two centers — one devoted to North Korea and the other to Iran. All but the counterintelligence unit fall under Pompeo's deputy on the CIA organizational chart.
Pompeo, who met with Russian intelligence officials in Moscow in May, would have been entitled to full briefings from the counterintelligence center even without making that bureaucratic tweak. But asserting more control of the unit responsible for preventing leaks probably pleased Trump, who has accused U.S. spy agencies of engaging in a smear campaign to undermine his presidency.
U.S. intelligence officials have disputed that spy agencies are behind such leaks but acknowledge broader concerns about security issues, pointing to episodes including the CIA's loss of a vast portion of its hacking arsenal, which was obtained this year by the anti-secrecy group WikiLeaks.
A descendant of the unit led by legendary CIA mole-hunter James Jesus Angleton, the counterintelligence center is run by a veteran female CIA officer who has served extensively overseas in Europe, East Asia and Russia. She was also one of the main authors of the CIA's internal review of a deadly suicide bombing that killed seven agency employees in Khost, Afghanistan, in 2009.
"I think she's wary about the administration," said a former colleague who also described her as "someone who would not fall in line" if she suspected interference in the center's role. Preventing the center from sharing information with the bureau would be difficult — an FBI official serves as head of the center's counterespionage unit.
Last year, the center played an important part in detecting Russian efforts to cultivate associates of the Trump campaign. Former CIA director John Brennan testified in May that he became "worried by a number of the contacts that the Russians had with U.S. persons" and alerted the FBI.
The center has since been enlisted to help answer questions about key moments in the timeline of Trump-Russia contacts, officials said, possibly including the meeting that Donald Trump Jr. held in June with a Russian lawyer.
"Who sent her on the mission — was it Russian intelligence or on her own initiative?" a former official said, referring to the lawyer, Natalia Veselnitskaya. "Mueller can't do anything on that without the agency."
Julie Tate, Adam Entous and Carol D. Leonnig contributed to this report.