The campaign group named Maj Gen Ahmadu Mohammed and eight other officers in a report last year, accusing the military of killing more than 8,000 detainees.
"It is unthinkable" to recall the officer, who was sacked in 2014, before an inquiry had even begun, it said.
The military is investigating the allegations, a spokesman told the BBC.
"These are just allegations - until proven, no-one should be punished unnecessarily," military spokesman General Rabe Abubakar said, confirming that Gen Mohammed had been reinstated.
Amnesty says Gen Mohammed was "in command of operations when the military executed more than 640 detainees following a Boko Haram attack on the detention centre in Giwa barracks on 14 March 2014".
He was sacked for unrelated reasons before recently being reinstated.
"Major General Mohammed must be investigated for participating in, sanctioning or failing to prevent the deaths of hundreds of people," Amnesty's secretary general Salil Shetty said in a statement.
But Gen Abubakar said the allegations were being investigated.
The London-based group said since March 2011, more than 8,000 young men and boys have been either shot, starved, suffocated or tortured to death in military custody and no-one has been held responsible.
President Muhammad Buhari promised to look into the issue when he came to power last year.
Boko Haram's Islamist insurgency has claimed thousands of lives and displaced more than two million people over the past six years.
In the latest incident, at least 65 people were killed and 136 injured when militants attacked the north-eastern Dalori village on Saturday night.
Boko Haram at a glance:
- Founded in 2002, initially focused on opposing Western-style education - Boko Haram means "Western education is forbidden" in the Hausa language
- Launched military operations in 2009
- Thousands killed, mostly in north-eastern Nigeria, hundreds abducted, including at least 200 schoolgirls
- Joined so-called Islamic State, now calls itself IS's "West African province"
- Seized large area in north-east, where it declared caliphate
- Regional force has retaken most territory this year
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