The airstrike, which occurred early today, triggered emotionally-charged protests in the provincial capital, with the victims' relatives rallying outside the governor's office while carrying the bodies of dead children.
The carnage underscores worsening insecurity after the Taliban last month overran Kunduz city for the second time in a year, as NATO-backed Afghan forces struggle to beat back the insurgents.
"Afghan forces and coalition troops conducted a joint operation against the Taliban insurgents," provincial spokesman Mahmood Danish told AFP. "In the bombardment 30 Afghan civilians were martyred and 25 others were wounded."
"They were asleep when their house came under attack by coalition troops," Akbari said.
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In a brief statement on Twitter, NATO conceded it was behind the airstrike.
"Airstrikes were conducted in #Kunduz to defend friendly forces under fire. All civilian casualty claims will be investigated," it said.
The strike occurred on the outskirts of the city after a firefight killed two US soldiers and three Afghan special forces during an anti-Taliban operation in Kunduz.
It was not immediately clear if the two incidents were related.
"On behalf of all of US Forces - Afghanistan, today's loss is heartbreaking and we offer our deepest condolences to the families and friends of our service members who lost their lives today," said John Nicholson, the top US and NATO commander in Afghanistan.
"Despite today's tragic event, we are steadfast in our commitment to help our Afghan partners defend their nation," he added, without disclosing the names of the dead soldiers.
During three lengthy debates between presidential candidates Hillary Clinton and Donald Trump, Afghanistan got scarcely a passing mention -- even though the situation there will be an urgent matter for the new president.
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