You are too scared to retrieve their bodies - this just proves you are the lady boys we always believed you to be
The move came after an Australian TV station ran footage of what it says was 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.
'Lady boys'
The SBS television footage begins with a warning of disturbing scenes, particularly for Muslim viewers.
You are too scared to retrieve their bodies - this just proves you are the lady boys we always believed you to be
It opens with what the programme describes as 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.
Some footage shows what the programme describes as the corpses of two Taleban fighters laid out facing Mecca and then being burned in what the reporter, John Martinkus, describes as a "deliberate desecration of Muslim beliefs".
Islamic tradition states that bodies should be washed, prayed for, wrapped in white cloth and buried within 24 hours.
The soldiers initially said they were burning the bodies for hygiene reasons, the programme reports.
We strongly condemn any disrespect to human bodies regardless of whether they are those of enemies or friends
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."
Guantanamo Bay
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".
Spokesman Col Jim Yonts said if true they were "reprehensible".
"The command does not advocate, nor does the command tolerate, the wrongful desecration of anyone's remains.
"The use of broadcast messages in conjunction with an act such as this does not represent the values and beliefs of this command therefore necessitating a procedural and policy review."
In May there were widespread demonstrations, 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.
The latest 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.
Afghanistan's Independent Human Rights Commission said US forces would be in breach of the Geneva Convention, which says that enemy dead should be honourably interred.
"It is outrageous. The Americans are ignoring the basic principles of international humanitarian law," the commission's deputy head, Ahmad Fahim Hakim, told the BBC.