A statement from the US military on Thursday said those killed in Shegal district in Kunar province were "al-Qaeda facilitators". It added that a child was also killed and a woman wounded.
Afghan officials, however, said the seven killed in the pre-dawn attack on a house were civilians.
US and Afghan troops were on an operation to capture suspected al-Qaeda operatives and said those killed and captured were linked to recent attacks on Afghan and US-led troops, the US military said.
"Afghan and coalition forces came under direct fire when approaching the compound and defended themselves with return fire," the US military said.
Provincial officials said that seven civilians that included village elders, were killed in an air strike.
Abdul Saboor, a senior provincial police officer, said the civilians where shot dead by US ground fire.
The US military said it had launched an investigation to determine the identity of those killed.
Since the US-led troops overthrew the Taliban in 2001, Taliban and al-Qaeda elements have been active in the province of Kuna, which is close to the border of Pakistan, a US military official said.
Pakistan said last week that the mastermind behind the foiled plot to blow up British airliners over the Atlantic two weeks ago was an al-Qaeda member based in Kunar.