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A total of five demonstrators were shot dead on Wednesday in anti-US protests in Afghanistan over the burning of the Koran at a US military base, officials said.

Three were killed in Shinwar district of Parwan province north of Kabul, provincial administration spokeswoman Roshna Khalid told AFP.

"The protests got violent. They attacked police with rocks and in a clash between police and protesters three people were killed and over 10 others are injured," Khalid said.

Two other people died in clashes between police and protesters in Kabul and in the eastern city of Jalalabad, health ministry and hospital sources said. In Jalalabad a group of students set fire to an effigy of US President Barack Obama.

Furious Afghans threw rocks and screamed "death to America", setting fire to shops and vehicles as gunshots rang out at the protests.

The US embassy in Kabul declared it was on lockdown and Afghan police said they were dispatching reinforcements to stop an angry mob torching cars and attacking shops, from marching into the centre of the capital.

Hundreds of people poured onto the Jalalabad road, throwing stones at US military base Camp Phoenix, where troops guarding the base fired into the air and black smoke from burning tyres rose, an AFP photographer said.

Afghanistan is a deeply religious country where slights against Islam have frequently provoked violent protests and Afghans were incensed that any Western troops could be so insensitive, 10 years after the 2001 US-led invasion.

The US commander in Afghanistan, General John Allen, apologised and ordered an investigation into the incident, admitting that religious materials, including Korans "were inadvertently taken to an incineration facility".

He also ordered that all troops would be trained in the "proper handling of religious materials no later than March 3".

US Defense Secretary Leon Panetta also apologised, saying that he and Allen "disapprove of such conduct in the strongest possible terms" and promising to "take all steps necessary and appropriate so that this never happens again".

The United States leads and dominates the 130,000-strong foreign military fighting a 10-year Taliban insurgency in Afghanistan.

Adding to pressure on US forces, It was also claimed Wednesday that nine schoolgirls were injured in a NATO helicopter attack in Afghanistan's eastern Nangarhar province.

NATO's International Security Assistance Force (ISAF) said it was looking into the allegation but had no immediate information.

"This morning a school was attacked by a NATO helicopter. Nine children, all girls, and the school's janitor have been injured," Ahmad Zia Abdulzai, the Nangarhar provincial government spokesman, told AFP.

"Some of the girls were discharged after receiving treatment but about five of them are still in the hospital," Abdulzai said, accusing the US-led ISAF force of carrying out the attack.

In Kabul, demonstrators attacked anti-riot police, forcing them to retreat, and shots were fired as the crowd tried to march on the centre of the capital, wounding at least 11 people, according to a health ministry official.

"Two of them are in critical condition," the official told AFP on condition of anonymity.

Police spokesman Ashmat Estanakzai denied police opened fire, but said the demonstration "got violent after they attacked Camp Phoenix" and blocked the key highway leading east towards the Pakistani border.

"They are marching toward Kabul. Police are trying to stop them. We have sent more reinforcements to the area."

The US embassy announced on its Twitter feed that it was on lockdown and that all travel was suspended.

"Please, everyone, be safe out there," it added.

A second protest erupted in west Kabul, involving about 100 university students, a police spokesman said.

In Jalalabad, there were pockets of demonstrations across the eastern city. Gunshots were heard but police did not confirm firing. Crowds threw rocks at cars and they set up fires in the streets, an AFP reporter said.

More than 1,000 demonstrators, many of them university students, blocked the highway shouting "Death to Americans, Death to Obama", an AFP reporter said.

Elsewhere in the country, about 800 gathered in district centre Baraki Barak in Logar province, a flashpoint for Taliban violence south of Kabul, shouting anti US slogans, said Sayed Wakil Agha, the district chief.

Reports that the Koran had been mistreated emerged on Tuesday, but it remains unclear exactly who was responsible.

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

AFP