The U.S. Energy Department has concluded that the Covid pandemic most likely arose from a laboratory leak, according to a classified intelligence report recently provided to the White House and key members of Congress.

The shift by the Energy Department, which previously was undecided on how the virus emerged, is noted in an update to a 2021 document by Director of National Intelligence Avril Haines’s office.

The new report highlights how different parts of the intelligence community have arrived at disparate judgments about the pandemic’s origin. The Energy Department now joins the Federal Bureau of Investigation in saying the virus likely spread via a mishap at a Chinese laboratory. Four other agencies, along with a national intelligence panel, still judge that it was likely the result of a natural transmission, and two are undecided.

The Energy Department’s conclusion is the result of new intelligence and is significant because the agency has considerable scientific expertise and oversees a network of U.S. national laboratories, some of which conduct advanced biological research.

The Energy Department made its judgment with “low confidence,” according to people who have read the classified report.

The FBI previously came to the conclusion that the pandemic was likely the result of a lab leak in 2021 with “moderate confidence” and still holds to this view.

The FBI employs a cadre of microbiologists, immunologists and other scientists and is supported by the National Bioforensic Analysis Center, which was established at Fort Detrick, Md., in 2004 to analyze anthrax and other possible biological threats.

U.S. officials declined to give details on the fresh intelligence and analysis that led the Energy Department to change its position. They added that while the Energy Department and the FBI each say an unintended lab leak is most likely, they arrived at those conclusions for different reasons.

The updated document underscores how intelligence officials are still putting together the pieces on how Covid-19 emerged. More than one million Americans have died in the pandemic that began more than three years ago.

The National Intelligence Council, which conducts long-term strategic analysis, and four agencies, which officials declined to identify, still assess with “low confidence” that the virus came about through natural transmission from an infected animal, according to the updated report.

The Central Intelligence Agency and another agency that officials wouldn’t name remain undecided between the lab-leak and natural-transmission theories, the people who have read the classified report said.

Despite the agencies’ differing analyses, the update reaffirmed an existing consensus between them that Covid-19 wasn’t the result of a Chinese biological-weapons program, the people who have read the classified report said.

A senior U.S. intelligence official confirmed that the intelligence community had conducted the update, whose existence hasn’t previously been reported. This official added that it was done in light of new intelligence, further study of academic literature and consultation with experts outside government.

The update, which is less than five pages, wasn’t requested by Congress. But lawmakers, particularly House and Senate Republicans, are pursuing their own investigations into the origins of the pandemic and are pressing the Biden administration and the intelligence community for more information.

Officials didn’t say if an unclassified version of the update would be issued.

U.S. national-security adviser Jake Sullivan, asked about the Journal’s reporting Sunday, said President Biden had repeatedly directed every part of the intelligence community to invest in trying to discern as much as possible about the origins of the pandemic. “President Biden specifically requested that the national labs, which are part of the Department of Energy, be brought into this assessment because he wants to put every tool at use to be able to figure out what happened here,” Mr. Sullivan said during an appearance on CNN.

There are a “variety of views in the intelligence community,” Mr. Sullivan added. “A number of them have said they just don’t have enough information.”

The Covid-19 virus first circulated in Wuhan, China, no later than November 2019, according to the U.S. 2021 intelligence report. The pandemic’s origin has been the subject of vigorous, sometimes partisan debate among academics, intelligence experts and lawmakers.

David Relman, a Stanford University microbiologist who has argued for a dispassionate investigation into the pandemic’s beginnings, welcomed word of the updated findings.

“Kudos to those who are willing to set aside their preconceptions and objectively re-examine what we know and don’t know about Covid origins,” said Dr. Relman, who has served on several federal scientific-advisory boards. “My plea is that we not accept an incomplete answer or give up because of political expediency.”

An Energy Department spokesman declined to discuss details of its assessment but wrote in a statement that the agency “continues to support the thorough, careful, and objective work of our intelligence professionals in investigating the origins of COVID-19, as the President directed.”

The FBI declined to comment.

China, which has placed limits on investigations by the World Health Organization, has disputed that the virus could have leaked from one of its labs and has suggested it emerged outside China.

The Chinese government didn’t respond to requests for comment about whether there has been any change in its views on the origins of Covid-19.

Some scientists argue that the virus probably emerged naturally and leapt from an animal to a human, the same pathway for outbreaks of previously unknown pathogens.

Intelligence analysts who have supported that view give weight to “the precedent of past novel infectious disease outbreaks having zoonotic origins,” the flourishing trade in a diverse set of animals that are susceptible to such infections, and their conclusion that Chinese officials didn’t have foreknowledge of the virus, the 2021 report said.

Yet no confirmed animal source for Covid-19 has been identified. The lack of an animal source, and the fact that Wuhan is the center of China’s extensive coronavirus research, has led some scientists and U.S. officials to argue that a lab leak is the best explanation for the pandemic’s beginning.

U.S. State Department cables written in 2018 and internal Chinese documents show that there were persistent concerns about China’s biosafety procedures, which have been cited by proponents of the lab-leak hypothesis.

Wuhan is home to an array of laboratories, many of which were built or expanded as a result of China’s traumatic experience with the initial severe acute respiratory syndrome, or SARS, epidemic beginning in 2002. They include campuses of the Wuhan Institute of Virology, the Chinese Center for Disease Control and Prevention, and the Wuhan Institute of Biological Products, which produces vaccines.

An outbreak at a seafood market in Wuhan had initially been thought to be the source of the virus, but some scientists and Chinese public-health officials now see it as an example of community spread rather than the place where the first human infection occurred, the 2021 intelligence community report said.

In May 2021, President Biden told the intelligence community to step up its efforts to investigate the origins of Covid-19 and directed that the review draw on work by the U.S.’s national laboratories and other agencies. Congress, he said, would be kept informed of that effort.

The October 2021 report said that there was a consensus that Covid-19 wasn’t the result of a Chinese biological-weapons program. But it didn’t settle the debate over whether it resulted from a lab leak or came from an animal, saying that more information was needed from the Chinese authorities.

The U.S. intelligence community is made up of 18 agencies, including offices at the Energy, State and Treasury departments. Eight of them participated in the Covid-origins review, along with the National Intelligence Council.

Before that report, the Energy Department’s Lawrence Livermore National Laboratory prepared a study in May 2020 concluding that a lab-leak hypothesis was plausible and deserved further investigation.

The debate over whether Covid-19 might have escaped from a laboratory has been fueled by U.S. intelligence that three researchers from the Wuhan Institute of Virology became sick enough in November 2019 that they sought hospital care.

A House Intelligence Committee report concluded last year that this disclosure didn’t strengthen either the lab-leak or the natural-origin theory as the researchers might have become sick with a seasonal flu. But some former U.S. officials say the sick researchers were involved in coronavirus research.

Lawmakers have sought to find out more about why the FBI assesses a lab leak was likely. In an Aug. 1 letter to FBI Director Christopher Wray, Sen. Roger Marshall, a Kansas Republican, requested that the FBI share the records of its investigation and asked if the bureau had briefed Mr. Biden on its findings.

In a Nov. 18 letter, FBI Assistant Director Jill Tyson said the agency couldn’t share those details because of Justice Department policy on preserving “the integrity of ongoing investigations.” She referred the senator to Ms. Haines’s office for information on what briefings were arranged for the president.