A press statement from the US forces said: "Coalition forces may have mistakenly killed and injured Afghan National Army soldiers last night in Khost province, Afghanistan."
The statement said that a joint investigation with the Afghan government and the Afghan national army would be mounted.
A communique from the Afghan defence ministry detailed the incident: "In an international military air strike at 2am [21:30 GMT on Tuesday] ... nine members of the Afghan National Army were martyred and three others were injured."
Colonel Greg Julian, a spokesman for the US Forces in Afghanistan, confirmed there had been an incident.
"There was an incident and we are getting together with ministry of defence officials to sort out exactly what happened. A joint investigation will be conducted to get to the truth," he said.
Under Nato command
There are about 60,000 international soldiers deployed under Nato and a separate force led by the UN in Afghanistan battling Taliban fighters.
The ministry did not specify which one of the deployments was responsible for the strike.
Most of the foreign troops operating in Khost are US armed forces operating under Nato and most air attacks are carried out by US aircraft.
In a separate development, Afghan officials claimed 35 Taliban-linked fighters and three police officers were killed in an attack in the southern Uruzgan province.
Juma Gul Hemat, Uruzgan's police chief, said heavy fighting began on Tuesday and continued into early Wednesday after the Taliban launched an attack on the area.
Hemat said around 100 fighters were involved in the battle.
However, Qari Youssef Ahmedi, a Taliban spokesman, disputed the police chief's figures, claiming they had lost seven fighters and killed 17 policemen in the attack.
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.