Protesters were faced by police who shot at them killing five people.
“Death to America”, chanted angered Afghans on Tuesday as they took to streets for a second day to protest against the US troops’ desecration of the holy Quran.
However, protesters were faced by police who shot at them killing five people.
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.
The US embassy in Kabul declared it was on lockdown and Afghan police said they were dispatching reinforcements to stop protesters.
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 tires.
Earlier, US occupation troops in Afghanistan had burned copies of the holy Quran in the airbase of Bagram.
The US commander in the war-torn country, General John Allen, apologized on Tuesday and ordered an investigation into the incident, admitting that religious materials, including copies of qoran "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".
For his part, US Defense Secretary Leon Panetta also apologized, 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".