WASHINGTON — The FBI is investigating the alleged unauthorized removal of classified documents from a secret CIA facility by Senate Intelligence Committee staff who prepared a study of the agency’s use of harsh interrogation techniques on suspected terrorists in secret overseas detention centers, McClatchy has learned.

The FBI’s involvement takes to a new level an extraordinary behind-the-scenes battle over the report that has hardened relations between the agency and its congressional overseers to their iciest in decades. The dispute also has intensified uncertainty about how much of the committee’s four-year-long study will ever be made public.

The FBI got involved after the CIA general counsel’s office requested the Justice Department start a criminal investigation into the removal last fall of classified documents by committee staff from a CIA high-security electronic reading room, which they needed to use to review top-secret emails and other materials, people familiar with issue told McClatchy. The existence of the referral was first reported online Thursday by Time magazine.

The matter is now with the FBI, said one federal official. Like all of those who spoke to McClatchy, the federal official requested anonymity because the case is highly sensitive, closely guarded and could potentially involve criminal charges.

The investigation request by the CIA general counsel’s office is one of two criminal referrals sent to the Justice Department in connection with the committee’s 6,300-page report, which remains unreleased nearly 15 months after the panel voted to approve its final draft, according to those familiar with the case.

The second was made by CIA Inspector General David Buckley, they said. It relates to the monitoring by the CIA of computers in the electronic reading room where the committee staff worked, they said.

It was unclear when precisely the referrals were made or when the FBI became involved or whether the bureau investigation also includes the computer monitoring.

The FBI and the CIA declined to comment. The committee referred calls to the Justice Department, which also declined to comment.

The committee’s $40 million classified study concluded that little valuable intelligence was obtained by the CIA’s use during the George W. Bush administration of waterboarding and other harsh interrogation methods on suspected terrorists in “black site” prisons in Europe, Africa, Asia and the Middle East, according to lawmakers who have read it.

The study, the lawmakers have said, also found that the CIA misled the White House, Congress and the public about the usefulness of the information gained from the techniques, which many experts and governments condemn as torture. The CIA and former Bush administration officials said the methods were legal. The program ended in 2006.

The committee approved a final draft of its report in December 2012 and submitted it to the CIA for an official response and recommendations on what portions should be withheld from the public. The agency submitted its response in June 2013 and has resisted its release, citing inaccuracies in some of the committee’s conclusions.

The dispute escalated last fall when committee staff discovered what lawmakers have characterized as a draft of a top-secret internal CIA review ordered by former CIA Director Leon Panetta that broadly corroborated their report’s findings, according to one of the knowledgeable people. They found the draft in a database into which documents were deposited after being vetted by a team of CIA officials and contractors.

The staff then realized that the draft review showed that CIA leadership misled the panel in submitting an official response that disputed some report conclusions, the knowledgeable person said. The staff printed out the draft and took it from the CIA facility to Capitol Hill, an act that the CIA regarded as the unauthorized removal of classified material and a violation of a user agreement between the sides, sources said.

The CIA confronted the committee in January with details of the unauthorized removal. The staff then determined that the CIA had recorded their use of the computers in the high-security research room that also allegedly violated the user agreement, McClatchy learned.

The CIA has denied that it conducted an internal review.