More than 2,000 people protested in front of the largest US-run military base in Afghanistan after hearing reports the troops had burned copies of the Koran. Hundreds of demonstrators also organised protests in Kabul.
Afghan protesters were angry after it was reported Nato troops who were working inside the base in Bagram, about 40 miles north of the capital Kabul, had set fire to copies of the Muslim holy book.
Some of the protesters threw petrol bombs and fired slingshots, while guards at the airbase responded by firing rubber bullets the AFP reported.
General John Allen, the US commander in Afghanistan has apologised over the incident, admitting that troops had "improperly disposed of a large number of Islamic religious materials which included Korans".
"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.
Allen added an investigation has now been launched.
"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 Korans," he said.
One protester told Reuters: "We Afghans don't want these Jewish infidels - they are the enemy of our soil, our honour and our Koran. I urge all Muslims to sacrifice themselves in order to pull out these troops from this soil".
Sidiq Siddiqi, an interior ministry spokesman, confirmed the demonstration and told the AFP that reinforcements were sent to the area to prevent possible violence.
Afghanistan is a conservative Muslim country where insult to the religion carries the death penalty.
The move is set to further bolster anti-US sentiments among Afghans.
There have been several cases of abuses by US and Nato troops since the invasion of Afghanistan in 2003.
In January a video showing what appear to be American forces urinating on dead Taliban fighters prompted anger and protests in Afghanistan.