USA and Afghan forces have conducted specific operations in recent months to target the Islamic State and drive them from eastern Afghanistan.
"Civilian casualties are totally unacceptable", said the UN's special representative in Afghanistan, Tadamichi Yamamoto, adding they demonstrate the importance of talks leading to a ceasefire and a permanent political settlement.
Sediq Sediqqi, spokesman for the presidential palace, condemned what he said was a suicide bomb attack. Insurgents were responsible for 62 percent.
The report said 2,563 civilians were killed and 5,676 were wounded in the first nine months of this year.
Khogyani said the victims include children who were at the mosque, and that the number of casualties could still rise.
The meeting was significant and the first that Khalilzad has held with the Taliban since last month, when President Donald Trump declared that the talks were 'dead, ' blaming an uptick in violence by the Taliban that included the killing of a United States soldier.