President Karzai accused Afghan and US led coalition forces yesterday of killing at least 89 civilians in an attack in the western province of Herat in what could be one of the worst cases of “collateral damage” in Afghanistan since 2001.

The US military said that 25 militants and five civilians, including two children, were killed in the ground attack and airstrike on Friday, and added that it was investigating reports of further noncombatant casualties.

An Afghan minister who visited the area put the civilian death toll at 90, a human rights group at the scene estimated it at 78 and the Interior Ministry reported 76 noncombatants dead, including 50 children.

A statement from President Karzai said: “In the tragic air strike and irresponsible and imprecise military operation in Azizabad village. . . more than 89 of our innocent countrymen, including women and children, were martyred.” Humayun Hamidzada, a spokesman for Mr Karzai, told The Times: “President Karzai strongly condemns this and has ordered a thorough investigation.” The President had dismissed General Jalandar Shah Behnam, the Afghan National Army general in charge of western Afghanistan, as well as a major in charge of Afghan commandos, he said.

Civilian casualties, especially from airstrikes, are among the main causes of friction between President Karzai and his Western backers — and fuel public antipathy towards both. Almost 700 civilians were killed in the first six months of this year, 255 of them by Afghan government and international troops, and the rest by Taleban militants, according to the UN.

Friday’s attack involved USled coalition forces, which mainly hunt al-Qaeda, as opposed to the Nato-led International Security Assistance Force, which is mainly fighting the Taleban and has stricter rules of engagement. A coalition spokesman told The Times that the operation was led by Afghan National Army commandos with air and ground support from the coalition, including a US C130 gunship overhead.

The coalition forces were trying to detain Mullah Siddiq, a mid-level Taleban commander in the area, who was presiding over a gathering of militants in the district of Shindad, said First Lieutenant Nathan Perry. They were ambushed as they approached the target and pursued their assailants back to the compound, before calling in an airstrike from the C130, Lieutenant Perry said. Afghan and foreign troops on the ground checked the battlefield afterwards and reported initially that 30 militants had been killed, including Mullah Siddiq, without any civilian deaths, he said. However, later on Friday they reported five civilian deaths — three women and two children believed to be Mullah Siddiq’s family.

The attacks sparked angry protests on Saturday from locals, who set fire to a police vehicle and waved banners reading “Death to America”. Local officials said many of the dead had gathered to mark the 40th day since the killing of a militia commander.

A council of religious leaders for western Afghanistan demanded yesterday that those behind the attack be put on trial and said it would call a demonstration in Herat today. It said in a statement: “Once again the enemies of Islam have stained their hands with the blood of innocent people. We, the Muslim nation, will not accept their apologies this time.”

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