The group says satellite images (above), provide indisputable and shocking evidence of the scale of last week's events.
The images show Baga and Doron Baga with almost 4,000 structures damaged or destroyed.
The attack is one of many by terrorist group Boko Haram, its members are currently trying to enforce an Islamist agenda in Nigeria.
They're efforts have led to many Christian areas and specifically churches being targeted.
Daniel Eyre, Nigeria researcher for Amnesty International, said: "These detailed images show devastation of catastrophic proportions in two towns, one of which was almost wiped off the map in the space of four days.
"Of all Boko Haram assaults analysed by Amnesty International, this is the largest and most destructive yet. It represents a deliberate attack on civilians whose homes, clinics and schools are now burnt out ruins.
"Up until now, the isolation of the Baga combined with the fact that Boko Haram remains in control of the area has meant that it has been very difficult to verify what happened there.
"Residents have not been able to return to bury the dead, let alone count their number. But through these satellite images combined with graphic testimonies a picture of what is likely to be Boko Haram's deadliest attack ever is becoming clearer.
"This week, Nigeria's Director of Defence Information stated that the number of people killed in Baga including Boko Haram fighters 'has so far not exceeded about 150'. These images, together with the stories of those who survived the attack, suggest that the final death toll could be much higher than this figure."
These attacks along with others have led to thousands of people fleeing violence across the border to Chad and to other parts of Nigeria including Maiduguri, the capital of Borno State.
They're increasing to the number, which is reported to be in the hundreds of thousands, who've become internally displaced or refugees.
Amnesty is calling on the governments of Nigeria and Chad to ensure these displaced people are protected and provided with adequate humanitarian assistance.