The police commander said six Afghan civilians died in the raid, near the border with Pakistan, while the US military said five "al-Qaida terrorists" had been killed.
"US bombardment on the border town of Mangaratay area of Barmal district killed six civilians on Friday," Paktika police chief Daulat Khan said in the Paktika capital Sharan, 160km south of Kabul, on Monday.
The US military later said five "terrorists" had been killed by coalition forces near Barmal district, denying there were any civilian casualties.
"We take our rules of engagement very seriously and I can assure you that these terrorists were no peaceful civilians," said military spokesman Lieutenant Colonel Bryan Hilferty.
US-led forces and Afghan soldiers returned fire when suspected fighters attacked US and Afghan National Army forces in Barmal area on Friday afternoon, the colonel said.
US army base at Shkin has been
dubbed 'the most evil place'
"We returned fire and killed five al-Qaida terrorists," he said.
Eight newly-trained Afghan National Army soldiers were also wounded and evacuated to one of the coalition's medical facilities.
Hilferty did not say whether the suspected fighters were killed by aircraft or ground forces.
Khan was unable to say what prompted the US warplanes to bomb Mangaratay, which lies a few kilometres from Barmal district, an area which was regained by a resurgent Taliban in August.
The Pakistan-based private Afghan Islamic Press (AIP) reported that the people were killed by firing from US jets as they travelled in a vehicle near the Afghan-Pakistan border.
The incident occurred less than 10km from the US army base at Shkin, dubbed "the most evil place in Afghanistan" by the US military because more US troops have been killed there than any other place in Afghanistan.
The porous 2450km Afghan-Pakistan border has been hard-hit by a wave of insurgency blamed on Taliban, their al-Qaida allies and supporters of former Afghan premier Gulbuddin Hekmatyar.
Scores of civilians have been killed in US-led bombing since the start of the US-led campaign against the Taliban regime and al-Qaida fighters in Afghanistan in October 2001.