The watchdog said: "Nato should create a body together with its Afghan partners and the United Nations to pursue justice for human-rights violations such as these".
It said the body should investigate allegations and ensure the prosecution of those found responsible and reparation for the victims.
Tim Parritt, Amnesty's deputy Asia Pacific director, said: "Isaf has a crucial role to play in securing the rule of law in Afghanistan.
"We urge Nato leaders to ensure that Isaf does not fall short of international humanitarian and human rights law in pursuing this aim."
The summit in Riga on Tuesday and Wednesday will focus on Nato's anti-Taliban operation in Afghanistan, the alliance's most ambitious mission yet.
Nearly 32,000 troops are in the 37-nation Isaf force, which has this year fought hard against the resurgent Taliban.
Isaf has made regular use of air strikes, which have killed scores of civilians in rural compounds, including 31 a month ago.
Human Rights Watch, the US human rights organisation, has said 1,000 civilians have been killed in the unrest this year, with an official report saying 3,700 people have been killed in total. Most of the dead are fighters.