The London-based rights group last year called for an investigation of nine senior commanders including Maj Gen Ahmadu Mohammed for possible criminal responsibility for war crimes including the deaths of more than 8,000 detainees since 2011.
Mohammed was commanding officer when soldiers killed around 640 unarmed detainees after Boko Haram extremists attacked Giwa barracks in northeast Maiduguri city, according to Amnesty.
President Muhammadu Buhari in June promised to investigate the allegations and deal with all alleged abuses by the military, but nothing has been done.
Mohammed was retired in 2014 after mutinying soldiers shot at him, revolting because they said a dozen colleagues killed by Boko Haram in a night ambush on the road from Chibok had been unnecessarily sent into danger.
More From This Section
The general was reinstated quietly in January, according to the military at his own request.
His reinstatement "makes mockery of commitments to end war crimes" and "underlines the monumental failure of the government to stamp out impunity for war crimes at the highest level.