The military never conducted an independent investigation into a 2019 bombing on the last bastion of the Islamic State, despite concerns about a secretive commando force.

In the last days of the battle against the Islamic State in Syria, when members of the once-fierce caliphate were cornered in a dirt field next to a town called Baghuz, a U.S. military drone circled high overhead, hunting for military targets. But it saw only a large crowd of women and children huddled against a river bank.

Without warning, an American F-15E attack jet streaked across the drone’s high-definition field of vision and dropped a 500-pound bomb on the crowd, swallowing it in a shuddering blast. As the smoke cleared, a few people stumbled away in search of cover. Then a jet tracking them dropped one 2,000-pound bomb, then another, killing most of the survivors.

It was March 18, 2019. At the U.S. military’s busy Combined Air Operations Center at Al Udeid Air Base in Qatar, uniformed personnel watching the live drone footage looked on in stunned disbelief, according to one officer who was there.

“Who dropped that?” a confused analyst typed on a secure chat system being used by those monitoring the drone, two people who reviewed the chat log recalled. Another responded, “We just dropped on 50 women and children.”

An initial battle damage assessment quickly found that the number of dead was actually about 70.

The Baghuz strike was one of the largest civilian casualty incidents of the war against the Islamic State, but it has never been publicly acknowledged by the U.S. military. The details, reported here for the first time, show that the death toll was almost immediately apparent to military officials. A legal officer flagged the strike as a possible war crime that required an investigation. But at nearly every step, the military made moves that concealed the catastrophic strike. The death toll was downplayed. Reports were delayed, sanitized and classified. United States-led coalition forces bulldozed the blast site. And top leaders were not notified.

The Defense Department’s independent inspector general began an inquiry, but the report containing its findings was stalled and stripped of any mention of the strike.

“Leadership just seemed so set on burying this. No one wanted anything to do with it,” said Gene Tate, an evaluator who worked on the case for the inspector general’s office and agreed to discuss the aspects that were not classified. “It makes you lose faith in the system when people are trying to do what’s right but no one in positions of leadership wants to hear it.”

Mr. Tate, a former Navy officer who had worked for years as a civilian analyst with the Defense Intelligence Agency and the National Counterterrorism Center before moving to the inspector general’s office, said he criticized the lack of action and was eventually forced out of his job.

The details of the strikes were pieced together by The New York Times over months from confidential documents and descriptions of classified reports, as well as interviews with personnel directly involved, and officials with top secret security clearances who discussed the incident on the condition that they not be named.