US Defence Secretary Donald Rumsfeld has urged military commanders to speed up their inquiry into claims that their troops burned Taleban corpses.
Reports of religious desecration have dented the US' image abroad
He said the longer it took to verify the allegations, the more harm it would do to the country's image abroad.
The probe was launched after soldiers were filmed allegedly desecrating two bodies and then taunting locals.
Mr Rumsfeld recalled the anger caused by past claims that Korans were defiled by guards at the Guantanamo Bay prison.
"The reality is that charges of that type are harmful," said the defence secretary, who was in Vilnius, Lithuania, for a Nato meeting.
"It's particularly disappointing when they're true. That needs to be determined, but one hates to see the adverse effect of it, if it is true.
"We also recognise the damage that can be done by the allegations alone, if they're not true."
But he said the alleged actions were not representative of the overwhelming majority of US servicemen and the positive contributions they have made.
Correspondents said the reaction in Afghanistan was muted so far but there were concerns the claims could spark off violent anti-US protests.
Afghanistan President Hamid Karzai said he was shocked by the report and called for a thorough inquiry.
The footage, captured by Australian TV channel SBS, purports to show the corpses of two Taleban fighters laid out facing Mecca and then being set alight.
The act of burning corpses is considered a sacrilege by Islam.
The soldiers initially said they were burning the bodies for hygiene reasons, the programme reports.
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."
There were widespread demonstrations in May throughout the Muslim world following reports that US forces had desecrated the Koran at the Guantanamo Bay military camp.