Defence ministry spokesman General Mohammad Zahir Azimi said Kabul was investigating after US forces allegedly set fire to the bodies of Taleban fighters, contravening Muslim traditions and international law.
If the investigation confirms the incident took place, "we will ask the US authorities to punish those responsible," Azimi told a press conference.
"It doesn't mean that we will ask the Americans to hand over those responsible but we will ask them to punish them under their own laws," he said.
Azimi said that Kabul hoped the burning of the bodies would be the last untoward incident involving US forces, who have regularly been accused of bombing civilians by accident during their ongoing campaign against the Taliban.
"We hope that the burning of Taliban bodies are the last (violations) to occur," Azimi said.
The US is also investigating the incident. The soldiers involved were reported to have taunted the Taliban over the burning, calling them "cowardly dogs" because they had not collected their comrades' bodies.
"You are too scared to retrieve their bodies. This just proves you are the lady boys we always believed you to be," said one message broadcast by the US, according to a report shown on Australian TV.
Washington has expressed deep concern over the incident, which follows criticism about the abuse of Afghan detainees in US custody and protests over reports that the Koran was desecrated at the US detention camp at Guantanamo Bay.
It has angered many in the conservative country despite near daily attacks by Taleban militants who launched an insurgency after they were removed from power in a US-led operation in 2001.
This year has been the bloodiest for militant-linked violence since the Taleban were removed, with around 1,400 people killed, many of the militants. A 17-year-old killed in a blast in Kandahar was the latest victim of the violence, Azimi said.
The United States is leading a coalition force of up to 20,000 troops who are helping Afghan forces to round up Taleban and al Qaeda fighters based mainly in the volatile south and east of the country.