The move came after an Australian TV station ran footage of what appeared to be US soldiers burning the remains.
The footage shows other troops apparently taunting residents of a nearby village, which they believed to be harbouring the Taleban.
The act of burning corpses is regarded as a sacrilege in Islam.
Afghan Defence Minister Abdul Rahim Wardak was "deeply shocked" at the report and has also ordered an inquiry, a spokesman said.
'Lady boys'
The SBS television footage begins with a warning of disturbing scenes, particularly for Muslim viewers.
It opens with shots of an American PsyOps unit using loud pop music to try to flush out the Taleban - who banned music when they ruled the country.
The most shocking footage in the film shows the corpses of two presumed Taleban fighters laid out facing Mecca and then being burned in what the reporter, John Martinkus, describes as a "deliberate desecration of Muslim beliefs".
| | You are too scared to retrieve their bodies - this just proves you are the lady boys we always believed you to be Troops' alleged message |
Later footage shows two US soldiers reading from a notebook messages which they said had already been broadcast to villagers.
"Attention Taleban you are cowardly dogs," the message reads. "You allowed your fighters to be laid down facing West and burnt.
"You are too scared to retrieve their bodies. This just proves you are the lady boys we always believed you to be."
A Pentagon spokesman said that, if true, the claims would be "very troublesome".
The US military condemned the alleged acts, saying they would be "aggressively investigated".
"This alleged action is repugnant to our common values, is contrary to our commands-approved tactical operating procedures, and is not sanctioned by this command," spokesman Maj Gen Jason Kamiya said.
In May, there were widespread protests, resulting in the deaths of at least 15 people in Afghanistan, after Newsweek magazine reported that US forces had desecrated the Koran at the Guantanamo Bay military camp.
'Outrageous'
The footage was shot in the village of Gonbaz outside the southern city of Kandahar by Australian cameraman Stephen DuPont, who was embedded with a US unit, for SBS's Dateline programme.
It shows a group of five soldiers standing on a rocky ledge, watching two burning corpses with arms and legs outstretched.
Islamic tradition states that bodies should be washed, prayed over, wrapped in white cloth and buried within 24 hours.
The soldiers initially said they were burning the bodies for hygiene reasons.
The TV report also suggests that the incident could be in violation of the Geneva Convention on the treatment of enemy remains, which states that the dead should be honourably interred.
Afghanistan's Independent Human Rights Commission called on US forces to find those accountable and punish them.
"It is outrageous. The Americans are ignoring the basic principles of the international humanitarian law," said its deputy head, Ahmad Fahim Hakim.
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