Fifty-five per cent of the deaths were attributed to anti-government forces and the remaining six per cent could not be attributed to any party, but included incidents such as people killed in crossfire, it said.
Thirty-eight aid workers were also killed in 2008, double the number of the previous year.
Death toll disputed
The overwhelming majority of deaths, 85 per cent, were caused by bombings, including those carried out by suicide bombers.
Nearly two-thirds of the 828 civilians allegedly killed by pro-government forces, died in air strikes targeting insurgents, the report said.
"Night-time raids, which sometimes result in death and injury to civilians, are of continuing concern and are widely resented in many communities," it said.
But the foreign forces in Afghanistan rejected the report's death toll.
A spokesman for Nato's International Security Assistance Force (Isaf) said only 237 civilians were killed by Isaf and the US-led force last year.
The large difference in the numbers was probably because of different methodologies used to collect data, Major Martin O'Donnell, the Isaf spokesman, was reported by the AFP news agency as saying.
Amid the escalating violence in Afghanistan, a Taliban commander and several of his associates were killed in an air raid on their compound in Herat province by US led forces on Tuesday.
|Foreign forces in Afghanistan have rejected the report's death toll [AFP]
Local officials told Al Jazeera that civilians, including an eight year-old child, had been killed in the raid.
The US military said it could not confirm the civilian casualties, but referred to the air raid as a "precision strike" on a Taliban target.
A British soldier was also killed on Tuesday after coming under fire in the province of Helmand, bringing to 35 the number of international soldiers killed in Afghanistan this year.
Isaf announced separately that its soldiers and Afghan police had captured two fighters in connection with a car bomb that killed two US soldiers in the eastern province of Khost a week ago.