The rights group called on Nigeria's government to investigate the deaths in the south-eastern city of Onitsha last month.
The Nigerian military described the claims as unfounded and misleading.
At least one million people died in the 1967-70 civil war started by Biafran secessionists. Protests have resumed over the past year.
According to Amnesty, some of those who died were members of the Indigenous People of Biafra (Ipob), a group campaigning for Biafran independence.
Some had been shot in the back, an indication that they were fleeing the scene, Amnesty said.
Ipob says Nigeria's government is dominated by northerners and has not done enough to develop the mostly Igbo-speaking south-eastern parts of Nigeria.