WASHINGTON — A Pentagon investigation into a U.S. airstrike in Syria in 2019 that killed dozens of people, including women and children, found that the military’s initial review of the attack was mishandled at multiple levels of command and replete with reporting delays and information gaps.

But the inquiry also determined that most of the people killed in the strike, which was carried out by a shadowy Special Operations unit called Task Force 9, were probably Islamic State fighters, according to three people familiar with the findings, and that military officials did not violate the laws of war or deliberately conceal casualties.

The findings did not call for any disciplinary action.

In response to the inquiry, Defense Secretary Lloyd J. Austin III ordered the military on Tuesday to improve the way it processes reports of civilian casualties. He said in a memo that he was “disappointed” in the handling of the initial review, which “contributed to a perception that the department was not committed to transparency and was not taking the incident seriously.”

Mr. Austin appointed Gen. Michael X. Garrett, the four-star head of the Army’s Forces Command, to lead the inquiry in November after an investigation by The New York Times described allegations that top officers and civilian officials had sought to hide casualties from the airstrike.

The attack, which took place on March 18, 2019, near the Syrian town of Baghuz, was one of the largest civilian casualty incidents in the yearslong war against the Islamic State, but the U.S. military had never publicly acknowledged it.

The Times’s investigation showed, though, that the military initially feared that dozens of people had been killed. A legal officer flagged the bombing as a possible war crime that required an investigation. The Defense Department’s independent inspector general began an inquiry, but the report containing its findings was stalled and did not mention the strike.

The military’s Central Command said in response to The Times’s reporting that the strike had been in self-defense against an imminent threat and that 16 fighters and four civilians had been killed. The command said it was not clear that the other people killed were civilians, in part because women and children in the Islamic State sometimes took up arms.

General Garrett’s inquiry is classified, and the Pentagon did not release its results. But the three people familiar with the findings said most of the other people killed were described as fighters, even though the Islamic State camp that was struck included women, children, captives and scores of wounded men who were no longer in the fight and, according to the law of armed conflict, were not legal targets.

In a two-page executive summary that the Pentagon released on Tuesday, General Garrett challenged The Times’s report, saying commanders followed procedures to determine that no civilians were in the blast zone before the strike. A senior Defense Department official acknowledged, however, that the military relied on faulty intelligence from Syrian partners, who said only combatants were in the area, and checked the target with a low-resolution drone camera that could not distinguish among the dozens of people sheltering in the area.

The three people familiar with the findings, who spoke on the condition of anonymity to discuss details of the confidential report, said that 56 people had been killed, but that 52 of them were enemy fighters, although that assessment classified all adult males in the strike as fighters, whether they were armed or not. The officials also said 17 people had been injured, 15 of whom were civilians.

The Baghuz attack was part of a series of investigations by The Times last year into airstrikes that killed civilians, including a botched drone strike in Kabul, Afghanistan, that killed 10 innocent people in August. Another Times investigation based on a trove of Pentagon reviews of strikes revealed systemic failures to prevent civilian deaths in the United States’ air war against the Islamic State.

Last week, the series was awarded the Pulitzer Prize for international reporting. John F. Kirby, the Pentagon spokesman, acknowledged that the reporting was “not comfortable, not easy and not simple to address.”

In response to The Times’s investigation, Mr. Austin ordered a standardized reporting process on civilian harm, the creation of a military “center of excellence” and the completion of a comprehensive new policy on the issue that has been in the works for more than two years. That policy review is still underway, with details of the initial plan expected by the end of June, Pentagon officials said.

“Protecting innocent civilians is fundamental to our operational success and is a strategic and moral imperative,” Mr. Austin said in his memo on Tuesday.

The Baghuz strike occurred in the last days of the offensive to clear Islamic State fighters from their self-proclaimed caliphate, which had once sprawled across areas of Syria and Iraq. American F-15 attack jets made repeated bombing runs on a riverbank where scores of women, children and wounded people had taken shelter.

Air Force personnel at a headquarters in Qatar who were watching drone footage taken from high above the site immediately reported the strike, saying that about 70 civilians may have been killed, and notified leaders that a formal investigation was required.

Instead, there was only a cursory report by the Special Operations unit responsible for the strike, which downplayed its impact, saying a handful of fighters had been killed and not mentioning civilian deaths. A formal investigation, conducted by the same unit, said four civilians had been killed and found no wrongdoing.

Air Force personnel who witnessed the strike later alerted the Defense Department inspector general’s office, which started an investigation.

General Garrett’s review identified a cascade of mistakes that led to the strike and the subsequent failures to accurately report the casualties.

At the time of the attack, the Islamic State was battling the U.S.-backed Syrian Democratic Forces, which called for U.S. airstrikes and said there were no civilians in the area. An American commander who launched the strike relied on faulty Syrian intelligence and blurry drone footage that did not reveal that scores of people were sheltering in the area, the senior Defense Department official said, adding that “if women and children had been reported in the area, they would not have taken that shot, period.”

The defense official acknowledged that the military did not respond in a timely manner, but said that General Garrett’s review did not find any “malicious or wrongful intent.”

Current and former military members who worked on thousands of airstrikes during the war against the Islamic State said that military personnel had been sounding alarms about several of the factors, including the unreliability of intelligence from the Syrian Democratic Forces and the overreliance on self-defense airstrike protocols.

“It’s the standard government line: Mistakes were made but there was no wrongdoing,” said Eugene Tate, a former evaluator for the Defense Department inspector general’s office who had tried looking into the Baghuz strike. “But if the same mistakes were being made over and over again for years, shouldn’t someone have done something about it? It doesn’t sit well with me, and I’m not sure it should sit well with anyone else.”

Mr. Tate, who said he was never interviewed for General Garrett’s investigation, said he witnessed Defense Department leaders trying to bury reports of the strike.

“The investigation says the reporting was delayed,” Mr. Tate said. “None of the worker bees involved believe it was delayed. We believe there was no reporting.”

In interviews, pilots, intelligence officers and members of a secret strike cell that ran much of the air war in Syria said the Baghuz attack was part of a disturbing pattern: Loopholes in regulations allowed Special Operations troops to speed up airstrikes against enemies, but a growing number of civilians were being killed.

At the start of the war against the Islamic State in 2014, top military leaders put in place a number of safeguards to minimize civilian harm. Drones studying targets were required to stay overhead for hours, collecting evidence that enemies were present and civilians were not. Strikes had to be approved by high-level officers.

But in 2016 and 2017, the authority to launch strikes was delegated down to the secret cell, which was run by the Army’s elite Delta Force. The cell, called Talon Anvil, found that it could shortcut these safeguards and strike at will by claiming self-defense. Soon nearly all of the cell’s strikes were justified under self-defense rules, even if they were miles from any fighting.

Current and former service members have been interviewed by criminal investigators from the inspector general’s office, according to people familiar with the inquiry.

A spokeswoman for the office, Megan G. Reed, said it could neither confirm nor deny the existence of a criminal investigation but added, “We are conducting a body of work in this area, and expect to release a report within a matter of months.”