The two soldiers allegedly punched the detainees on the chest, shoulders and stomach while they were being held at a base in Uruzgan province, a statement said on Sunday. Neither detainee required medical attention, it said.
"The command remains committed to investigate all allegations of misconduct and will hold individuals responsible for their actions consistent with US military law," Brigadier-General Jack Sterling, a deputy coalition commander, was quoted as saying.
The charges include conspiracy to maltreat, assault and dereliction of duty. The allegations, if substantiated, could lead to disciplinary action, the statement said.
US military spokesman Lieutenant-Colonel Jerry O'Hara said the alleged assault occurred in early July.
He said the two soldiers were still in Afghanistan "performing their primary duties, but they have nothing to do with detained individuals".
"The command remains committed to investigate all allegations of misconduct and will hold individuals responsible for their actions consistent with US military law"
Brigadier-General Jack Sterling,
Deputy coalition commander
One of the two detainees has since been released, while the other is being held at Bagram, the US military's headquarters in Afghanistan, about 30km north of the capital, Kabul.
The allegations come 10 days after the US military launched an investigation into allegations that troops burned the bodies of two Taliban rebels slain in battle, an act that was purportedly caught on video by an embedded freelance cameraman.
Cremation is banned in Islam, and the alleged desecration, which was broadcast on television, sparked outrage in Afghanistan.
Some Muslim clerics warned of a violent anti-American backlash, but there have been no demonstrations.