"Now we have 11 dead and over 50 other people admitted with injuries to hospital," acting provincial health director Hassan Basij told AFP.
Police opened fire at protests in Taloqan, capital of the usually peaceful northeastern province of Takhar, after NATO-led forces said they killed four insurgents including two armed women in an overnight raid in the town.
A spokesman for the International Security Assistance Force (ISAF) in Kabul said the raid targeted the Islamic Movement of Uzbekistan (IMU), a militant group that operates from bases including in Afghanistan.
But the protesters claimed those killed during the NATO raid were civilians.
The issue of civilian deaths during international military operations is highly sensitive in Afghanistan and has drawn repeated, sharp criticism from Afghan President Hamid Karzai.
It was not immediately clear whether those who died at the demonstrations were killed by police bullets or those from another source.
Lal Mohammad Ahmadzai, a regional police spokesman, blamed "some opportunists and violence-seeking elements" for infiltrating the protests and turning them violent.
Interior ministry spokesman Zemarai Bashary told AFP in Kabul: "There have been demonstrations, about 2,000 have demonstrated over the operation overnight. The demonstrations have turned violent."
Bashary said the protestors threw rocks at the Provincial Advisory Team (PAT) compound, where around 40 German soldiers are based.
PATs are foreign-led teams that work to help Afghan government institutions in particular areas to improve their performance.
Although relatively peaceful compared to Taliban strongholds in the south, the north of Afghanistan has seen an increase in violence in recent years.
Seven UN staff were killed when a protest against the burning of the Koran in the US turned violent last month and their compound in the northern city of Mazar-i-Sharif was stormed.
Afghan and NATO forces have said that central Asian militant groups such as the IMU are active in the region.
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