The call by the rights group followed a report in the Times of London newspaper on Friday citing confidential UN reports that more than 20,000 civilians were killed by Sri Lankan army shelling.
The report followed weeks of allegations that large numbers of civilians had been killed as the army closed in on Tamil Tiger rebels to end the decades- long war.
Amnesty's Asia Pacific director Sam Zarifi accused both sides of war crimes and called for an independent international probe.
"The Times report underscores the need for this investigation and the UN should do everything it can to determine the truth about the ˜bloodbath’ that occurred in northeast Sri Lanka," Zarifi said in statement.
The statement said the UN "must immediately publicise its estimate of the number of civilians killed by the two sides in the final weeks of fighting".
Sri Lanka's Human Rights Minister Mahinda Samarasinghe dismissed Amnesty's call and said the organisation was being "ridiculous to keep har