Colonel Greg Julian, a spokesman for the US-led coalition forces in Afghanistan, said a joint investigation into the incident is under way.
"Initial reports from troops on the ground indicate that this may be a case of mistaken identity on both sides," a statement from his office said.
The soldiers' deaths are the latest from a series of air raids which have killed scores of civilians and police.
In July, nine Afghan policemen were killed in air raids by international forces after troops clashed with police in the southwestern province of Farah.
Both sides had mistaken the other for Taliban and al-Qaeda-linked fighters.
Hamid Karzai, Afghanistan's president, called for a review of regulations for international forces in the country after at least 90 civilians were killed in US attacks in a western village in August, according to Afghan and UN figures.
A US military investigation concluded that at least 33 civilians, including a dozen children, died in the air raid, along with 22 opposition fighters.
About 60,000 international troops from Nato and a separate US-led coalition are currently stationed in Afghanistan in an attempt to crush Taliban and al-Qaeda-linked fighters opposed to the government in Kabul.
The Taliban was in government between 1996 and 2001 and has gained ground in the south of the country in recent months.
Over two days of fighting that ended on Wednesday, 35 Taliban fighters were killed by police in Dih Rahwud, a district in the southern province of Uruzgan, police said.
"Our police bravely resisted and killed 35 Taliban whose bodies are left in the area," Juma Gul Hemat, the provincial police chief, said.
"Three of our policemen were also martyred and nine others were injured in the fighting," he said.
Also on Wednesday, three soldiers from the US-led coalition were killed when their vehicle hit a roadside bomb in the west of the country, the headquarters of US forces in Afghanistan said.
"Coalition personnel secured the scene, and the incident is under investigation," it said in a press release issued in Kabul.