It said the UN had failed to deliver justice to the relatives of the victims, despite being charged by the security council with protecting human rights in the region.
The UN assumed administration of Kosovo after Serbia relinquished control in 1999, when Nato chased Serbian out of the region with a brutal three-month bombing campaign.
About 1,800 people went missing during the war, which left 10,000 dead.
Hundreds of Kosovan Serbs were abducted and most of them killed in revenge attacks by ethnic Albanian fighters after Nato-led troops were deployed and the UN took over.
The UN passed over most of its police responsibilities in Kosovo to an EU mission in 2008 after Kosovo claimed independence from Serbia.
The Amnesty report - a rare look at the plight of Serbs in Kosovo immediately after the conflict - listed several cases in which UN administrators failed to investigate atrocities.
The security council is due to debate Kosovo tomorrow.
The "failure to investigate what constituted a widespread systematic attack on a civilian population and potentially crimes against humanity has contributed to the climate of impunity prevailing in Kosovo," said Amnesty International Kosovo specialist Sian Jones.
For nearly a decade, UN police and prosecutors had "failed to initiate prompt, effective, independent, impartial and thorough investigations."