The U.S.-led NATO strike hit two villages in the Bala Buluk district on Monday while conducting an "antiterrorist operation." At least 124 civilians, most of them children, women and elderly were killed.
Protesters threw stones at government buildings chanting anti-American slogans such as "Death to U.S." and "Americans, go away from Afghanistan," and demanding the arrest of those guilty of the massacre.
Local media said the protests in the Farah province turned violent, prompting police to fire warning shots. As a result, three demonstrators received gunshot wounds.
Police said the airstrike took place during an intense battle between Taliban militants and local police on Monday and Tuesday near the village of Ganj Abad in Bala Buluk district, a Taliban-controlled area near the border with Iran.
The local police chief, Abdul Ghafar Watandar, said some 30 militants and three police officers died in the battle, while four police officers and several government soldiers were wounded.
The Afghan massacre has been criticized by international organizations, including the Red Cross. Following a meeting with Afghan President Hamid Karzai in Washington on Wednesday, President Barack Obama expressed U.S. regret over the incident, although the foreign troops in Afghanistan have yet to comment.
Afghanistan's government has been increasingly critical of U.S.-led strikes that have led to major civilian losses. According to the United Nations, 552 civilians were killed by NATO airstrikes in Afghanistan in 2008.
In a separate incident in the Gereshk district in the country's southern Helmand province, a suicide bomber killed 12 and injured about 30 people, a security official said.
The bomber attacked an international military vehicle. A NATO spokesman confirmed the attack, but did say whether there were troop casualties.
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