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The US military on Friday said it had killed al-Qaeda's emir for northeastern Afghanistan in an airstrike last month, in a major blow to the group as it seeks to re-establish safe havens in the country.

Pentagon spokesman Peter Cook described the assault that killed Farouq al-Qahtani as a "precision strike" and said it took place on October 23 in Kunar, Afghanistan.

"This successful strike is another example of US operations to degrade international terrorist networks and target terrorist leaders who seek to attack the US homeland, our interests and our allies abroad," Cook said in a statement.

He said another al-Qaeda leader in the country, Bilal al-Utabi, was targeted in a separate strike, though the results of that attack were not yet known.

Last month, US officials said multiple Hellfire missiles had leveled two compounds in Kunar where the men were believed to be hiding.

One US official said the attack represented the most significant strike against the al-Qaeda leadership in Afghanistan in years.

The Pentagon has been actively hunting for Qahtani for four years. He had longstanding ties with Osama bin Laden before his death in the 2011 US raid on his Pakistan compound.

Qahtani has operated in Afghanistan since at least 2009 and led an al-Qaeda battalion since at least mid-2010.

His deputy Utabi was seen as the second- or third-most senior Al-Qaeda leader in Afghanistan.

On Thursday, US airstrikes killed at least 30 Afghan civilians in the northern province of Kunduz after a Taliban attack left two American soldiers dead.

The strike triggered emotionally charged protests in the provincial capital, with the victims' relatives parading mutilated bodies of dead children piled into open trucks through the streets of Kunduz city.

A US defense official, speaking on condition of anonymity, said "multiple" manned US planes were involved in the strikes, and they were targeted by small-arms fire from the ground.

Civilian casualties caused by NATO forces have been one of the most contentious issues in the 15-year campaign against Taliban insurgents, prompting strong public and government criticism.

Errant airstrikes contributed to a 42 percent jump this year in casualties caused by pro-government forces compared to last year, according to the UN.

Agencies contributed to this report