The report said militants were responsible for 55 percent of the deaths, but that U.S., NATO and Afghan forces killed 829 civilians, or 39 percent.
Civilian deaths have been a huge source of friction between the U.S. and President Hamid Karzai, who has increased demands that U.S. and NATO troops avoid killing civilians during operations.
As President Barack Obama prepares to send troops to war for the first time as commander in chief,in to save the faltering international campaign.
Close toto secure two violent provinces near Kabul have begun operations in the field and already are seeing combat, the unit's spokesman said Monday.
The U.S. and Afghan militaries this month announced plans to increase the number of Afghans who will take part in U.S. operations, a step aimed at reducing deaths of ordinary Afghans.
The U.N.'s annual report on the protection of civilians noted that despite new battlefield rules meant to reduce civilian casualties, U.S., NATO and Afghan troops killed 31 percent more civilians in 2008 than in 2007, when the U.N. said those forces killed 629 civilians.
"As the conflict has intensified, it is taking an increasingly heavy toll on civilians," the U.N. said.
Militants increasingly rely on roadside bombs, car bombs and suicide bombers, attacks that are "frequently undertaken regardless of the impact on civilians," the report said.
But U.S., NATO and Afghan operations also have resulted in an increase in civilian casualties, "notwithstanding efforts to implement policies and procedures to minimize the impact of their operations on civilians," the report said.
The U.N. report said militants were responsible for 55 percent of civilian deaths last year, or 1,160. About 130 deaths couldn't be accounted for because of issues like crossfire.
A U.S.-based group that advocates for civilians in conflict said in a new report released Tuesday that "the lack of a clear, coordinated strategy to address civilian losses has been a leading source of anger and resentment toward military forces" in Afghanistan.
"The international coalition in Afghanistan is losing public support, one fallen civilian at a time," CIVIC, or The Campaign for Innocent Victims in Conflict, said.
The United States military and other members of the NATO-led force in Afghanistan make some condolence payments to the families of civilians accidentally killed in battle. But CIVIC said that a "significant number" of families receive no help from international forces and that anger is especially strong when no help is provided.
"Every family with losses not recognized and addressed is another obstacle to Afghanistan's stabilization and development," the report said.
The CIVIC report urged the Pentagon to create a position to address civilian casualties, and it said the NATO-led force in Afghanistan should have a coordinated response to provide compensation payments to the families of victims.