The enraged crowd shouted "Death to Americans" and "Death to infidels" on Tuesday as guards at Bagram Airbase, north of Kabul, responded by firing rubber bullets from a watchtower, said an AFP photographer, who was hit in the neck.

Hundreds of other people protested in the Afghan capital as security forces dispatched reinforcements in a bid to stop the demonstrations from spiralling out of control in the fiercely conservative Muslim country.

The US commander in Afghanistan, General John Allen, apologised and ordered an investigation into a report that troops "improperly disposed of a large number of Islamic religious materials which included Qur'ans".

"I offer my sincere apologies for any offence this may have caused, to the president of Afghanistan, the government of the Islamic Republic of Afghanistan, and most importantly, to the noble people of Afghanistan," he said.

The White House also apologised, calling it "a deeply unfortunate incident" while US Defence Secretary Leon Panetta promised a swift investigation.

Two US officials, who spoke on condition of anonymity, told AFP the military removed Qur'ans from the US-run prison at Bagram because inmates were suspected of using the sacred book to pass messages to each other.

"The material was removed because there was a concern that the detainees were communicating with each other," one US official said.

Allen did not mention how the religious materials had been disposed of, but an AFP photographer was shown partly-burnt copies of the Koran said to have been saved from destruction by Afghan workers within the base.

Allen's remarkably candid statement, apparently aimed at damage control after similar incidents led to violence and attacks on foreigners, was played repeatedly on Afghan television.

Afghan President Hamid Karzai in a statement said he "strongly condemns the burning of copies of the Qur'an by American soldiers" and had assigned a delegation to investigate the incident.

The Taliban, who have been waging a decade-long insurgency against Karzai's Western-backed government, also condemned the Qur'an burning, accusing the Americans of "hurting the religious feelings of one billion Muslims throughout the world".

Iran described the actions as "an insult to the holy Qur'an".

"The only solution to restore calm and stability is the swift departure of foreign troops from the country," foreign ministry spokesman Ramin Mehmanparast said, according to the website of state television.

Allegations that NATO troops at Bagram had set fire to copies of the Muslim holy book were first reported by Afghans working at the base, a senior government official said.

A local police official said more than 2,000 people were demonstrating outside the sprawling US-run Bagram base at one stage.

The AFP photographer saw at least seven protesters hit by rubber bullets, some of them bleeding.

Sediq Sediqqi, an interior ministry spokesman, said Afghan security forces brought the demonstration under control and that by late afternoon it was over.

He said one young protester had been wounded, but had no further details.

Last April, 10 people were killed and dozens of others were injured during days of unrest unleashed by the burning of a Qur'an by American pastor Terry Jones in Florida.

Allen's statement reflected concern over the impact of the latest incident in the country, where US troops are battling Taliban insurgents and supporting Karzai's government.

"I have ordered an investigation into a report I received during the night that ISAF personnel at Bagram Airbase improperly disposed of a large number of Islamic religious materials which included Qur'ans," he said.

"When we learned of these actions, we immediately intervened and stopped them. The materials recovered will be properly handled by appropriate religious authorities.

"We are thoroughly investigating the incident and we are taking steps to ensure this does not ever happen again. I assure you -- I promise you -- this was NOT intentional in any way."

Allen thanked "the local Afghan people who helped us identify the error, and who worked with us to immediately take corrective action".

Last month, US officials scrambled to condemn four US soldiers shown in an online video urinating on the bloodied corpses of three Taliban insurgents.

The video, including one of the soldiers saying "Have a great day, buddy", served as a reminder of previous abuses committed by US troops during the war.

Copyright AFP (Agence France-Presse), 2012