The US force in Afghanistan later issued a statement regretting the incident and describing it as a "tragic case of mistaken identity on both parts".
A statement from the US force said that while undertaking an operation against a Taliban fighter, they responded to gunfire from a building close by.
"Coalition forces engaged those firing with small-arms fire and coalition aircraft. It was later determined those firing on the force were ANP [Afghan National Police]," the statement said.
"Coalition forces deeply regret the incident of mistaken fire. Initial reports indicate this was a tragic case of mistaken identity on both parts," Colonel Jerry O'Hara, US Forces Afghanistan spokesman, said in the statement.
The Afghan police thought that the US forces were the Taliban undertaking an attack.
"Unfortunately, the special forces didn't inform the police that they were going to the village,'' Gulab Shah Alikhail, Zabul's deputy governor, said.
The US said the target of Wednesday's raid was an opposition commander "known to co-ordinate attacks against coalition forces along Highway One',' Afghanistan's main highway that circles the country.
A joint investigation involving Afghan and US-led forces has been opened into the incident.
Native security forces and civilians have been the victim of attacks by US-led forces many times before.
Nine Afghan soldiers were killed in late October by US bombs in a similar operation in Khost province.