WASHINGTON — Senators, spies and a president spent years in a pitched battle over how the history is told of one of the most controversial chapters of America’s campaign against terrorism, the detention and interrogation of prisoners in secret C.I.A. jails.
But recent moves by the Trump administration have increased the likelihood that much of what is known about the macabre humiliations that unfolded in those jails around the world will remain hidden from public view.
Congressional officials said on Friday that the administration had begun returning to Congress copies of a 6,700-page Senate report from 2014 about the C.I.A. program. The move raises the possibility that most of the copies could be locked in Senate vaults indefinitely or even destroyed — and increases the risk that future government officials, unable to read the report, will never learn its lessons.
The classified report is the result of a lengthy investigation into the program by Democrats on the Senate Intelligence Committee, telling the story of how — in the years after the Sept. 11, 2001, terrorist attacks — the C.I.A. began capturing terrorism suspects and interrogating them in secret prisons beyond the reach of the American judicial and military legal systems. The central conclusion of the report is that the spy agency’s interrogation methods — including waterboarding, sleep deprivation and other kinds of torture — were far more brutal and less effective than the C.I.A. described to policy makers, Congress and the public.
The Trump administration’s decision honors the request of the Republican chairman of the Senate Intelligence Committee, Richard M. Burr of North Carolina, who has portrayed the report as shoddy and excessively critical of the C.I.A. and the administration of President George W. Bush. The F.B.I., the Office of the Director of National Intelligence, the C.I.A. and the agency’s inspector general have returned their copies of the report, said American officials who asked not to be named to discuss the status of those classified copies.
The report is the most comprehensive accounting of the Bush-era program that exists. A declassified executive summary was made public in December 2014, and it laid bare some of the worst excesses of the war on terrorism, drawing broad condemnation both inside the United States and abroad.
Officials who played important roles in the C.I.A. detention program remain at the agency, including its newly appointed deputy director, Gina Haspel, and the former head of the agency’s counterterrorism center, Michael D’Andrea. Mr. D’Andrea recently assumed control of the agency’s Iran operations.
The Senate Intelligence Committee, which was run by Democrats when the executive summary was released, sent copies of the entire report to at least eight federal agencies, asking that they incorporate it into their records — a move that would have made the documents subject to requests under the Freedom of Information Act. That law, which allows citizens, the news media and other groups to request access to information held by the federal government, does not apply to congressional records.
The agencies all refused to add the report to their records, and instead kept their copies locked up, prompting the American Civil Liberties Union to sue the C.I.A. for access to the full report.
Some Republicans on the panel supported the publication of the 500-page executive summary. Others issued a rebuttal that challenged some of the conclusions — but not specific facts — in the report, such as the finding that the interrogation methods did not produce useful intelligence.
After Republicans took over the Senate in early 2015, Mr. Burr asked the Obama administration to return all the copies that had been sent to the C.I.A., the Pentagon, the Justice Department and other executive-branch agencies.
The Obama administration instead left the matter to the courts, and the case was still being heard when President Trump took office on Jan. 20. It was decided in April, with a ruling that cleared the way for the agencies to return their copies to the Senate.
Mr. Burr has called the report nothing more than a “footnote in history.” His committee is now conducting one of the investigations into whether any of Mr. Trump’s campaign advisers or associates assisted in the Russian effort to disrupt last year’s presidential campaign.
The return of the report to the Senate committee “is extremely disturbing on a number of levels,” said Katherine Hawkins, senior counsel at the Constitution Project, an advocacy organization. “First, it remains absurd that no one in the executive branch will open the full report. Second, Senator Burr’s ongoing attempts to bury the torture report casts doubt on his willingness to follow the facts to conclusions that would damage the administration in the Russia probe.”
The C.I.A., the F.B.I. and the Office of the Director of National Intelligence declined to comment.
The full report is not expected to offer evidence of previously undisclosed interrogation techniques, but the interrogation sessions are said to be described in great detail. The report explains the origins of the program and identifies the officials involved, and also offers details on the role of each agency in the secret prison program.
It remains an open question what Mr. Burr will do with the copies that are returned to the Senate. He said on Friday that the committee would “enact necessary measures to protect the sensitive sources and methods contained within the report.”
During his confirmation process to become director of the C.I.A., Mike Pompeo told the Senate Intelligence Committee that he would read the full report.
Democrats on the committee expressed fear that the report would be buried — or worse, that electronic copies would be erased and hard copies destroyed.
“No senator — chairman or not — has the authority to erase history. I believe that is the intent of the chairman in this case,” said Senator Dianne Feinstein, Democrat of California, who was the committee’s chairwoman when the report was written.
Some on the Democratic side also expressed frustration with what they considered the tepid response of the committee’s Democratic vice chairman, Senator Mark Warner of Virginia. They said Mr. Warner felt it was more important to preserve his relationship with Mr. Burr for the sake of the Russia investigation than to battle over the detention report.
Mr. Warner said in a statement on Friday that the report was “a thorough, fact-based and straightforward history.”
He added, “This study must be preserved for history.”
At least three copies remain outside Senate hands, though they are off limits to the public.
In December, President Barack Obama notified the Senate that he was including a copy of the full report in his presidential records, which would be deposited at the National Archives and Records Administration.
That copy was still at the archives on Friday, said James B. Pritchett, a spokesman for the agency. But presidential records are generally not eligible to be made public until 12 years after the president leaves office — and even then, classified documents, like the report, could remain secret indefinitely.
A second copy is in the hands of the Pentagon. A judge overseeing the military commission prosecution of five Guantánamo Bay detainees accused of aiding the Sept. 11 attacks — each of whom was previously held by the C.I.A. — ordered the Defense Department in January to hold on to a copy.
And a third, which had been held by the Justice Department, is now at the Federal District Court of the District of Columbia. Late in the Obama administration, two judges on that court ordered the administration to hand over a copy in response to requests by lawyers for two other former C.I.A. detainees who are now being held at the Guantánamo Bay prison. The lawyers argued that preserving the report was necessary for their legal cases.
The Trump administration complied with the order in February, depositing the copy with the court’s security officer.
The Senate had also given the Justice Department a copy of the report for the F.B.I. The bureau has returned that copy to the Senate, officials said.
The return of the F.B.I. copy could raise questions about whether Attorney General Jeff Sessions was abiding by a pledge he made during his confirmation process not to return the Justice Department’s copy to the Senate.
But a spokeswoman for Mr. Sessions, Sarah Isgur Flores, noted on Friday that the other copy once held by the Justice Department is with the Federal District Court, not the Senate.