MAZAR-I-SHARIF, Afghanistan — The atrocities of the Afghan civil war in the 1990s are still recounted in whispers here — tales of horror born out of a scorched-earth ethnic and factional conflict in which civilians and captured combatants were frequently slaughtered en masse.

Stark evidence of such killings are held in the mass graves that still litter the Afghan countryside. One such site is outside Mazar-i-Sharif, in the north. It lies only half-excavated, with bones and the remains of clothing partially obscured by water and mud from recent flooding. Experts say at least 16 victims are here, and each skull that lies exposed is uniformly punctured by a single bullet-entry hole at the back.

The powerful men accused of responsibility for these deaths and tens of thousands of others — some said to be directly at their orders, others carried out by men in their chain of command — are named in the pages of a monumental 800-page report on human rights abuses in Afghanistan from the Soviet era in the ’80s to the fall of the Taliban in 2001, according to researchers and officials who helped compile the study over the past six years....