US-led forces killed six men during a night raid in the southern Afghan province of Zabul, but Afghan officials disputed a US military account that the victims were Taliban fighters.
Mohammad Hashim, a member of Zabul's provincial council, said that the dead men belonged to two families and were not involved in militancy.
A US military statement said the operation was aimed at Taliban insurgents and the "ensuing engagement resulted in six militants killed".
Though supported by the West, President Hamid Karzai's government has been undermined by civilian casualties inflicted by Western forces fighting the Taliban.
Karzai faces dwindling public support, with a presidential election due in August, analysts say.
Afghanistan has seen a sharp escalation of violence in recent years and is going through its bloodiest period since US-backed forces overthrew the Taliban in late 2001.
About 2,100 Afghan civilians were killed last year, more than a third of them by foreign and Afghan forces, according to the United Nations.
The Taliban insurgency flared back into life in 2005, a year after Karzai's election, and US President Barack Obama has laid new emphasis on stabilising Afghanistan and denying space for al Qaeda to regather its strength.
There are nearly 70,000 foreign troops under Nato and US command trying to quell the Taliban and the United States is expected to nearly double its force in Afghanistan from 36,000 to more than 60,000 within 18 months.
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