A Royal Australian Air Force F-18 Super Hornet receives fuel from a KC-10 Extender over Iraq in July. (Staff Sgt. Larry Reid Jr./U.S. Air Forces Central Command Public Affairs)

The attack aircraft — American A-10s, Australian F-18 Hornets and Danish F-16s — converged over eastern Syria in the late afternoon. Their target: several clusters of Islamic State militants, dug in among rocky hills overlooking a strategic airfield.

For nearly an hour, the aircraft successively struck the sites below, laying waste to trenches, sandbagged fighting positions, vehicles and tanks, holding at a distance between bombing runs. Higher in the sky, British and American drones kept a constant watch.

The planes were still pounding their targets when leaders at the U.S. air command center in Qatar got a call from a Russian liaison officer: They were hitting Syrian army troops, not the Islamic State.

Accusations that the Sept. 17 attack killed at least 60 members of President Bashar al-Assad’s army struck a blow to the U.S.-led air campaign’s claims of accuracy, inflamed U.S.-Russia tensions and threatened to bury a faltering cease-fire deal.

In the hours after the attack, the Pentagon issued a statement of regret, and a senior officer is now investigating the attack, which may mark the first Western strike on government forces in Syria.

The incident underscores the difficulties that military commanders face as they conduct an air campaign in a nation where they have little ground presence and where an array of armed factions clash across constantly changing battle lines.

The Syrian government has seized on the incident as a chance to propagandize about U.S. perfidy, asserting that it proves Western support for the Islamic State. The authorities’ list of alleged casualties, anti-government activists allege, includes long-dead soldiers whose deaths they had been trying to hide.

The picture is further complicated by the fact that some within the U.S. military say the initial statement of regret may have been premature, suggesting that all indications — including what the individuals struck were wearing and what they were doing — point to the possibility that at least some of those killed may have been militants.

“We were pretty convinced they were ISIL moving through ISIL territory,” one U.S. official said, speaking on the condition of anonymity to speak freely. ISIL is an acronym for the Islamic State.

But interviews with Syrians and U.S. officials with knowledge of the strike provide new detail about an operation that took place in a hotly contested area, where Islamic State, Syrian army and pro-government militia forces had been positioned in close quarters. The attack marks one of only a handful of times since 2014 when the U.S.-led coalition has struck an active fault line between Syrian and Islamic State forces.

Faysal Itani, a scholar at the Atlantic Council, a Washington think tank, said a central question is: “Why did we make such a serious error?”

The strike came amid a sustained U.S. air campaign across Deir al-Zour’s vast desert, which seeks to deprive the militants of oil assets and roads they could use to strengthen campaigns elsewhere.

While government-militant clashes have been a regular fact of life in Deir al-Zour, the Jabal al-Tharda highland is seen as especially important for both sides, said Jalal al-Hamad, who heads an activist organization tracking events there.

Their seizure, he said, “would mean capture of the airport and the falling of areas controlled by the regime.”

Militant have tried repeatedly to capture the highland and, at least twice, they succeeded in driving off government forces. But according to statements by Syrian officials, pro-government troops and local activists, the Syrian army and supporting militiamen were in place there when the strike occurred.

On Friday, Russian Foreign Minister Sergei Lavrov said the situation in Deir al-Zour had been “static” for two years and dismissed U.S. claims that the area had been under aerial surveillance for two days before the strike. “Government troops surrounded by ISIL, and that’s it,” he said. “If this is a mistake after two full days of intelligence and of targeting, then we also want an investigation, frankly speaking.”

The militiamen’s presence may have been critical to any error. According to Aymenn Jawad Al-Tamimi, a fellow at the Middle East Forum, a U.S. think tank, the Syrian army, sapped by five years of relentless fighting, receives vital support in Deir al-Zour from a host of pro-government irregulars, including militia groups,religious factions and tribal groups. Some of those groups wear regular uniforms; some do not.

U.S. officials say both Islamic State and Syrian fighters were present but thought they could distinguish between the two.

Assad has insisted the attack on established army positions could not have been a mistake. “It was definitely intentional,” he said in an interview with the Associated Press published on Thursday.

Typically, targeteers and intelligence personnel combine imagery taken from drones, manned surveillance planes or satellites with electronic surveillance and reports from intelligence assets or friendly forces.

But Norton A. Schwartz, who was the U.S. Air Force chief of staff from 2008 to 2012, said the task of identifying factions on the ground becomes harder when those forces do not wear traditional uniforms or when they use weapons and equipment that differs from those of known military forces.

Unlike other areas of Syria where the United States conducts airstrikes, there also is no real U.S.-backed armed opposition force in Deir al-Zour, making it more difficult for the United States to obtain reliable on-the-ground reporting.

“The truth of the matter is that we can hit whatever we aim at. The real fundamental question is, is it the right target?” Schwartz said. “That is a human undertaking, both for intelligence and operations.”

Before the attack, an official at the coalition air command center in Qatar phoned a Russian official at a military base in Syria and informed him of the general location where the strike would occur. U.S. officials notify the Russian military of strike plans in certain cases, including when they say that government forces may be in the area.

About 20 minutes after the first bomb was dropped, a Russian official called back, saying he had something to pass along to the designated liaison officer.

By the time the U.S. officer spoke with the Russian official, who informed him that coalition planes might be hitting Syrian government forces, almost an hour had gone by. Less than five minutes later, commanders gave the order to cut the short operation.

At the Pentagon, senior officials were aghast, worrying the incident might derail a hoped-for cease-fire between the Syrian government and opposition forces. The Pentagon was already on the defensive over its barely veiled opposition to negotiating a deal with Russia that would have led to unprecedented military cooperation with Moscow.

Fady Mallah, who leads a pro-government militia that was present at Jabal al-Tharda, said that Islamic State forces were not far from where Syrian fighters were hit. He said a large number of militants were at “shooting distance” — about 200 meters, he said, from pro-government forces at the time of the attack.

After the strike, men identified as Syrian soldiers described it on Syrian television, saying they had observed surveillance planes all day before the strikes began in the late afternoon. Their positions, which included trenches, security walls, tanks and vehicles, were struck more than 12 times, they said from a hospital in Deir al-Zour.

“At first, we thought they were our planes,” one young fighter told a pro-government news channel from his bed. “Then they started hitting us. . . . All our colleagues were killed.”

Pro-government websites have posted names of the alleged victims in last week’s attack, saying that two major-generals and three colonels were killed. Some local media reported that conscripted prisoners were also among the dead.

Activists, however, have voiced doubt in the government’s account of the attacks, saying far fewer dead and wounded were received at a nearby military hospital.

Hamad and other activists have suggested the Syrian government has included casualties from earlier engagements in its count of the Sept. 17 dead. That would allow it to explain away the deaths of senior officers that would raise questions about the government’s narrative of the war.

“We think it was an attempt to cover up casualties from previous battles,” he said.

Habib reported from Berlin. Liz Sly in Beirut, Zakaria Zakaria in Istanbul, Karen DeYoung in New York and Louisa Loveluck, Thomas Gibbons-Neff, Suzan Haidamous and Dana Priest in Washington contributed to this report.