WASHINGTON — President Trump’s order allowing Attorney General William P. Barr to declassify any intelligence that sparked the opening of the Russia investigation sets up a potential confrontation with the C.I.A., effectively stripping the agency of its most critical power: choosing which secrets it shares and which ones remain hidden.
On Friday, Dan Coats, the director of national intelligence, said the agencies under his purview would give the Justice Department “all of the appropriate information” for its review. But Mr. Coats, a seasoned politician, also included a not-so-subtle warning that his agency’s secrets must be protected.
“I am confident that the attorney general will work with the I.C. in accordance with the long-established standards to protect highly-sensitive classified information that, if publicly released, would put our national security at risk,” Mr. Coats said, referring to the intelligence community.
Mr. Trump granted Mr. Barr’s request for sweeping new authorities to conduct his review of how the Trump campaign’s ties to Russia were investigated. The president ordered the C.I.A. and the other intelligence agencies to cooperate, granting Mr. Barr the authority to unilaterally declassify their documents and thus significant leverage over the intelligence community.
Mr. Trump defended his decision earlier on Friday, telling reporters as he left for a trip to Japan that the declassification would be sweeping. “What are we doing, we are exposing everything,” he said. “We are being transparent.” He expressed no qualms about national security implications.
As Mr. Coats’ comments suggested, intelligence officials believe the danger of the move by Mr. Trump, was that it could endanger the agency’s ability to keep the identities of its sources secret.
The most prominent of those source among them may well be a person close to President Vladimir V. Putin of Russia who provided information to the C.I.A. about his involvement in Moscow’s 2016 election interference.
The concern about the source, who is believed to be still alive, is one of several issues raised by Mr. Trump’s decision to use the intelligence to pursue his political enemies. It has also prompted fears from former national security officials and Democratic lawmakers that other sources or methods of intelligence gathering — among the government’s most closely held secrets — could be made public, not because of leaks to the news media that the administration denounces, but because the president has determined it suits his political purposes.
Intelligence officials have feared before that their findings were being twisted to political agendas — notably concerns during the run-up to the Iraq war that information about Saddam Hussein’s alleged weapons of mass destruction was being cherry-picked to justify combat. But Mr. Trump’s decision is different.
It allows Mr. Barr, who has used the charged term “spying” to describe efforts to investigate the Trump campaign, sole discretion to declassify the intelligence behind the F.B.I.’s decision to begin investigating whether any Trump aides or associates were working with the Russians. It also raises the specter that officials ranging from the F.B.I. to the C.I.A. to the National Security Agency, which was monitoring Russian officials, will be questioned about their sources and their intent.
The order could be tremendously damaging to the C.I.A. and other intelligence agencies, drying up sources and inhibiting their ability to gather intelligence, said Representative Adam Schiff, Democrat of California and the chairman of the House Intelligence Committee.
“The president now seems intent on declassifying intelligence to weaponize it,” Mr. Schiff said in an interview.
Mr. Trump has long held that he was a target of the “deep state,’’ at various points accusing former President Barack Obama without evidence of tapping his phones, the F.B.I. of secretly trying to undermine his candidacy and past intelligence chiefs of bending their findings to prove Russian involvement in his election victory.
He has repeatedly appeared to side with Mr. Putin’s contention that there is no evidence of a Russian campaign to sabotage the 2016 election, even though the Mueller report left no question that the Russian leadership was behind both the theft and publication of emails and other data from Democrats and a social media campaign that ultimately worked to boost Mr. Trump’s candidacy, as well as efforts to tamper with election registration systems.
But it is the human source that particularly worries some former and current intelligence officials. Long nurtured by the C.I.A., the source rose to a position that enabled the informant to provide key information in 2016 about the Russian leadership’s role in the interference campaign.
John O. Brennan, the C.I.A. director under Mr. Obama, would bring reports from the source directly to the White House, keeping them out of the president’s daily intelligence briefing for fear that the briefing document was too widely disseminated. Instead, he would place them in an envelope for Mr. Obama and a tiny circle of aides to read.
The source provided evidence for one of the last major intelligence conclusions that Mr. Obama made public before leaving office: that Mr. Putin himself was behind the Russia hack.
John Sipher, a former C.I.A. official who led Russia operations for the agency, expressed concern that giving the president names of sources or agency officials who oversaw those informants could put those secrets at risk because they would inevitably be more widely disseminated.
“If the president of the United States asks for a name, it would be hard not to provide a name,” Mr. Sipher said. “It wouldn’t do him any good unless he sent it around to people to look into it, and that is where the security problem is, obviously.”
Mr. Schiff pledged that his committee would pay close attention to all of Mr. Barr’s actions in the inquiry. “We are going to expose any abuse, any politicization of intelligence,” he said.