America's most senior soldier in Afghanistan has called for the Pentagon to investigate claims that more than 90 civilians were killed in an American airstrike, after harrowing video footage emerged showing the broken bodies of at least 11 children among the dead.

The grim, eight-minute clip, filmed on a mobile phone in the aftermath of the bombing, shows rows of shrouded bodies laid side by side in a make-shift morgue. Among them are at least 11 children, many of them toddlers.

General David McKiernan, the commander of Nato's International Assistance Force (Isaf), ordered a fresh investigation led by a Pentagon general after footage was released on Sunday night. In a statement he said: "In light of emerging evidence pertaining to civilian casualties ... I feel it is prudent to request that US Central Command send a general officer to review the US investigation and its findings."

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The top-level review comes just days after he admitted there were "large discrepancies" among accounts of the death toll. American officials claim there were just seven civilians killed. The United Nations, the Afghan government and human rights groups said that the body count was closer to 90. Locals said most of the dead were women and children.

The damning footage was shot by a doctor who visited the morgue, in a building normally used as a mosque, on the morning after the attack on 22 August.

At one point a blanket is pulled back to show the grey, lifeless face of an infant. The dead child's head is no bigger than a man's hand. A large section of skull is missing. Women can be heard wailing in the background. One mourner is heard crying for his mother.

The bombs were called in by American Special Forces after their patrol was ambushed in Azizabad, in Herat province, shortly before dawn on that day. Officials said the American soldiers were trying to arrest a suspected Taliban commander.

Days after the attack, American officials remained adamant that just 30 Taliban insurgents had been killed, including their commander, despite detailed claims by Afghan officials that at least 76 people were killed, including 50 children.

Four days after the airstrike, on 26 August, the UN's senior official in Kabul, Kai Eide, claimed he had "convincing evidence ... that some 90 civilians were killed, including 60 children, 15 women and 15 men".

Hamid Karzai, Afghanistan's President, said relations with the United States had "worsened" in the wake of the raid, which prompted a grovelling phone call from President George Bush.

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There has been growing criticism of international troops for failing to curb civilian killings. A report by Human Rights Watch, published yesterday, said civilian deaths as a result of airstrikes by the US and Nato tripled from 2006 to 2007, which have sparked a public backlash.

Brad Adams, the group's Asia director, said: "Mistakes by the US and Nato have dramatically decreased public support for the Afghan government and the presence of international forces."

American officials eventually revised their initial body count, on 2 September, but they were still nowhere close to the numbers reported elsewhere. A spokesman said: "The investigation found that 30 to 35 Taliban militants were killed. In addition five to seven civilians were killed, two civilians were injured and subsequently treated."

Mr Eide, the UN's Special Representative, summoned General McKiernon to his office in Kabul on Friday last week to see the evidence for himself. General McKiernon was furious that the UN had released such an uncompromising statement condemning the raid. But a source close to the Isaf commander revealed he was almost moved to tears when he finally saw the images for himself. "He was shocked and humbled. He left like a little boy," the military aide said.

If the 90 dead are confirmed, it would be the worst incident of collateral damage in Afghanistan since US and UK forces invaded in 2001.

Missiles fired by US drones killed 16 people, in an attack launched across the border into Pakistan yesteday. The strike targetted a religious school founded by an old friend of Osama bin Laden, intelligence officials and Pakistani villagers said. The US has increasingly used drones to make cross broder strikes on suspected Taliban targets in recent weeks. The missile killed 16 people, most of them Pakistani and Afghan Taliban fighters, though four women and two children were also killed, according to a senior intelligence officer.