It said those forces had deliberately demolished civilian homes and forcibly displaced inhabitants "with no justifiable military grounds".
Although the Kurdish People's Protection Units (YPG) pushed back against the allegations at the time, it said on Tuesday that it would prosecute four of its fighters accused of damaging property in a town recaptured by ISIL several months ago.
All three provinces mentioned in Amnesty's latest report on Iraq are outside the borders of the autonomous Kurdistan region.
However, Kurdish forces gained or solidified control over areas in the provinces after federal troops fled ISIL's devastatingly effective offensive in June 2014.
Iraqi Kurdish leaders want to incorporate territory from the provinces into their autonomous region, and depopulating them of Arabs aids efforts to solidify Kurdish control.
Baghdad strongly opposes Iraqi Kurdistan's incorporation of the areas, which it wants to remain under federal control, but after fighting ISIL for these areas, the Kurds are even more committed to keeping them.