The alleged massacre took place between December 12 and 14 last year, following a confrontation between members of the Islamic Movement of Nigeria (IMN) and soldiers in Zaria, in the northern central Kaduna state.
Amnesty also dismissed army claims that IMN members had been seeking to kill the head of the army.
The confrontation happened in December in Zaria between the IMN and the army after the army tried to pass a roadblock set up by the Islamic Movement.
Amnesty International have uncovered evidence on the ground revealing buildings were razed, people were burnt alive and people were dumped in mass graves.
"The army went and surrounded the location where the protesters were, and deliberately shot, including with heavy weapons, for hours, throughout the night into the following day, deliberately killing unarmed men women and children. People who were too badly injured to escape were burnt alive, when soliders set fire to the buildings," Donatella Rovera, the Amnesty International's Senior Crisis Response Adviser, who wrote the report, told RFI.
"And then, the army went to great lengths to destroy the evidence: they destroyed the buildings they had been firing at for 24 hours, and which they then burnt. That would have been crucial evidence. They then buried the bodies in mass graves. Amnesty International has uncovered a site, which we believe is where hundreds of people are buried."
She heard this from interviewing over 90 witnesses on the ground. Furthermore, satellite images of the site taken on 2 November and 24 December 2015, show disturbed earth spanning an area of approximately 1000 square metres and the complete destruction of buildings and mosques.
"The places where everything happened have been incredibly thoroughly cleaned up. I have investigated many massacres over the years, but I don't think I've ever come across a situation where the perpetrators had gone to such an extent to destroy and remove the evidence," Rovera said.
"The neighbours told us that the authorities washed the streets so that there was no blood left after the bodies were picked up. We saw that all the rubble of the properties they destroyed, was removed. There were no bullets or bullet casings on the streets... There is no doubt that they were aware of the terrible crimes that have been committed and they did all they could to cover it up."
Unfortunately this is not unheard of in Nigeria. It is not the first time the army is accused of such a massacre. But our attempts to reach the army and the government failed.
"The army either does nothing or it smashes something. So, it is not a subtle tool. I think that it has been a reliably tense situation for some time now, the sect would block the road, quite frequently, and there are a lot of Nigerians who think that in fact they had it coming because this was regularly happening, that people would come in contact with this sect and that it was only a matter of time," Andrew Walker, a writer who's been covering Nigeria for over ten years, told RFI.
"This is a fairly standard way of mopping up after something like this, these kind of things happen all too frequently in Nigeria and the fairly standard way of dealing with it is to round everybody up, bury them in a massive grave and hope the whole thing goes away and well, hope that no one cares."
Donatella Rovera said what is probably different with this mutiny is the fact that it has nothing to do with Boko Haram.
There, the targets were Shiite muslims. The leader of the group has been detained ever since.
"The government actually rather than coming and clamping down on these sort of abuse by its army, it actually supports it. And up to this very day, the IMN leader Al-Zakzaky, who was shot four times and is blind from one eye now due to the lack of treatment after his left eye popped out of its socket and had to be pushed back in, is still under detention," Massoud Shadjareh, a member of the Islamic Human Rights Commission, who's been travelling in Nigeria recently, told RFI.
"Right now, it's been four months since he has been held, not by the police, not by the army, but by the security forces... He has had no access to legal processes, nor medical care, and really, this is against international law and against the contitutional law of Nigeria."
He added that this is quite worrying because the Nigerian army works with the UN and is involved in the African Union peace keeping exercises.
He further begged the question, if they can do this to their own civilians, what's to be expected of their behaviour in other countries.