Seven people have been killed and at least 76 injured during three days of violent demonstrations, all of them in clashes with security forces and police in towns east of the capital Kabul.
Angry Afghans shouting "Death to America" poured on to the streets of Kabul on Thursday for the first time as protests at the reported desecration also broke out in 10 of the country's 34 provinces.
The United Nations and foreign aid agencies evacuated hundreds of workers from Jalalabad fearing further violence.
Two protesters were killed when gunfire broke out as police stopped them from marching into the eastern city of Jalalabad, deputy governor of Nangarhar province Mohammad Asif Qazizada said.
Newsweek alleged the Quran was
descretaed in Guantanamo Bay
Another person died and four were wounded when rioters attacked a police station in the Chak district of Wardak province, Interior Ministry spokesman Lutfullah Mashal said.
The protests were sparked by a small report in Newsweek magazine last week stating that interrogators at the US military detention centre in Guantanamo Bay desecrated copies of the Quran by leaving them in toilet cubicles and even stuffing one down a lavatory to rattle Muslim prisoners.
The controversy has also spread to Pakistan, where demonstrations were held in Peshawar and Quetta, two major cities close to the border with Afghanistan.
The US has promised to investigate the desecration claim.
US Secretary of State Condoleezza Rice on Thursday called disrespect for the holy book abhorrent and promised to punish offenders.
"If they are proven true, we will take appropriate action. Respect for religious freedom for all individuals is one of the founding principles of the United States"
US secretary of state
"Our military authorities are investigating these allegations fully," Rice said. "If they are proven true, we will take appropriate action. Respect for religious freedom for all individuals is one of the founding principles of the United States."
But the top US military officer said a review of interrogation logs has so far found no evidence to corroborate the explosive allegations.
"They cannot confirm yet that there was ever the case of the toilet incident except in one case, a log entry that they still have to confirm, where a detainee was reported by a guard to be ripping pages out of a Quran and putting them in a toilet to stop it up as a protest," said General Richard Myers, the chairman of the Joint Chiefs of Staff.