The Times investigation found that the bombing had been called in by a classified American special operations unit, Task Force 9, which was in charge of ground operations in Syria. The task force operated in such secrecy that at times it did not inform even its own military partners of its actions. In the case of the Baghuz bombing, the American Air Force command in Qatar had no idea the strike was coming, an officer who served at the command center said.

In the minutes after the strike, an alarmed Air Force intelligence officer in the operations center called over an Air Force lawyer in charge of determining the legality of strikes. The lawyer ordered the F-15E squadron and the drone crew to preserve all video and other evidence, according to documents obtained by The Times. He went upstairs and reported the strike to his chain of command, saying it was a possible violation of the law of armed conflict — a war crime — and regulations required a thorough, independent investigation.

But a thorough, independent investigation never happened.

This week, after The New York Times sent its findings to U.S. Central Command, which oversaw the air war in Syria, the command acknowledged the strikes for the first time, saying 80 people were killed but the airstrikes were justified. It said the bombs killed 16 fighters and four civilians. As for the other 60 people killed, the statement said it was not clear that they were civilians, in part because women and children in the Islamic State sometimes took up arms.

“We abhor the loss of innocent life and take all possible measures to prevent them,” Capt. Bill Urban, the chief spokesman for the command, said in the statement. “In this case, we self-reported and investigated the strike according to our own evidence and take full responsibility for the unintended loss of life.”

The only assessment done immediately after the strike was performed by the same ground unit that ordered the strike. It determined that the bombing was lawful because it killed only a small number of civilians while targeting Islamic State fighters in an attempt to protect coalition forces, the command said. Therefore no formal war crime notification, criminal investigation or disciplinary action was warranted, it said, adding that the other deaths were accidental.

But the Air Force lawyer, Lt. Col. Dean W. Korsak, believed he had witnessed possible war crimes and repeatedly pressed his leadership and Air Force criminal investigators to act. When they did not, he alerted the Defense Department’s independent inspector general. Two years after the strike, seeing no evidence that the watchdog agency was taking action, Colonel Korsak emailed the Senate Armed Services Committee, telling its staff that he had top secret material to discuss and adding, “I’m putting myself at great risk of military retaliation for sending this.”

“Senior ranking U.S. military officials intentionally and systematically circumvented the deliberate strike process,” he wrote in the email, which was obtained by The Times. Much of the material was classified and would need to be discussed through secure communications, he said. He wrote that a unit had intentionally entered false strike log entries, “clearly seeking to cover up the incidents.” Calling the classified death toll “shockingly high,” he said the military did not follow its own requirements to report and investigate the strike.