Police fired into the air in an attempt to disperse demonstrators on the biggest protests since unrest erupted last week over plans by a US pastor to burn the Koran. The pastor has since suspended the plan.
"There are more than 10,000 of the demonstrators and some of them are waving the Taliban flag," police officer Mohammad Usman said.
The protests come three days before a parliamentary election which the Taliban have vowed to disrupt. The election is a key test of stability in Afghanistan before US president Barack Obama conducts a war strategy review in December.
They follow three days of protests at the weekend over plans by Florida Pastor Terry Jones, which he later abandoned, to burn copies of the Koran to mark the anniversary of the September 11th, 2001, hijacked airliner attacks on the US.
Three people were killed in those protests. Observers including the top UN diplomat in Afghanistan had warned the Taliban may try to exploit the Koran-burning protests.
A police source later said one person had been killed and five wounded, and that the toll could rise.
The protests were the Reuters television pictures showed protesters waving large white flags, the symbol used by Taliban supporters. A spokesman for the the Taliban, Zabihullah Mujahid, said group was aware of the protests but had no role in them.
"People may have raised the Taliban flags to show their sentiment and sympathy for the Taliban," he said.
At the Pul-e-Kandahari, or Kandahar bridge in Kabul, police were ordered to advance towards one group of hundreds of protesters who were throwing stones and shouting "Death to American slaves" at police.
Police were seen firing into the air and dragging away several protesters. At one point, volleys of gunfire could be heard. The protesters scattered, some sheltering in nearby houses in the mainly ethnic Pashtun and Tajik area of Kabul.
The protesters earlier gathered in the west of the capital, burning tyres and blocking a main highway link to the south.
Thick black smoke rose above the area and police kept journalists several hundred metres back. Witnesses at the scene saw two unconscious people, covered in blood, being carried away suffering what appeared to be gunshot wounds.