More than 580,000 refugees have fled to neighbouring Bangladesh since August 25 after the Myanmar Army launched a military offensive following attacks on multiple government posts by Rohingya rebels.
Myanmar's government said it was responding to attacks by Muslim insurgents, but the UN and the international community called the response "disproportionate".
In its report, Amnesty cited testimony from more 120 Rohingya men and women who fled to Bangladesh in recent weeks, the Guardian reported.
"In this orchestrated campaign, Myanmar's security forces have brutally meted out revenge on the entire Rohingya population of Rakhine state, in an apparent attempt to permanently drive them out of the country," said Amnesty International Crisis Response Director Tirana Hassan.
"These atrocities continue to fuel the region's worst refugee crisis in decades."
"Exposing these heinous crimes is the first step on the long road to justice. Those responsible must be held to account," she added, specifically calling for Myanmar's Commander-in-Chief, senior general Min Aung Hlaing, to take immediate action to stop his troops from committing atrocities.
Thirty medical professionals, aid workers, journalists and Bangladeshi officials were also interviewed for the research, titled "My World Is Finished", and Amnesty also referred to satellite imagery as well as on-the-ground video footage.
Myanmar blocked media and major UN aid agencies from operating freely in Rakhine and satellite images from Human Rights Watch showed that at least 288 villages were partially or totally destroyed by fire in Rakhine.
Amnesty said eyewitnesses of the worst violence "consistently implicated specific units, including the Myanmar Army's Western Command, the 33rd Light Infantry Division, and the Border Guard Police" and that troops were sometimes joined by local vigilantes.
The body said it documented murder, deportation and forcible displacement, torture, rape and other sexual violence, persecution and other inhumane acts such as denying food and other life-saving provisions, which are all considered crimes against humanity at the International Criminal Court.
Following the Arakan Rohingya Salvation Army (ARSA) attacks on August 25, Myanmar security forces surrounded Rohingya villages in Rakhine and opened fire, killing or seriously injuring hundreds of people, Amnesty said.
This was repeated in "in dozens of villages across Maungdaw, Rathedaung, and Buthidaung townships".
Amnesty said it had documented the killings of a dozen people in Chein Kar Li, Koe Tan Kauk and Chut Pyin villages in Rathedaung Township, in Inn Din, Min Gyi and in Maungdaw Township. The death toll was highest in Chut Pyin and Min Gyi where the organisation estimates scores were killed.
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