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"Security forces did not commit shooting at innocent villagers and sexual violence and rape cases against women. They did not arrest, beat and kill the villagers," the report said. It also cleared security forces of robbing Rohingya, as well as burning their mosques and villages.
"There is overwhelming evidence that the military has murdered and raped Rohingya and burned their villages to the ground," Amnesty said.
"After recording countless stories of horror and using satellite analysis to track the growing devastation we can only reach one conclusion: these attacks amount to crimes against humanity."
The military said the report, which posted on the military's official Facebook page, was based on interviews with more than 2,800 Rohingya and other ethnic groups between October 13 and November 7.
The report comes as Myanmar's State Counselor Aung San Suu Kyi met for a bilateral discussion with US Secretary of State Rex Tillerson on Tuesday behind closed doors.
The two met in Manila during the 31st summit of the Association of South-east Asian Nations, or ASEAN. Following the meeting they shook hands in front of waiting media but didn't take any questions.
Tillerson will be heading to Myanmar on Wednesday where US officials say he will push for a solution to end the violence against the Rohingya.
'They killed and killed and piled the bodies up high'
In an exclusive CNN report published Monday, refugees described surviving mass killings and rape before reaching the relative safety of the camps, where conditions are dire.
"They killed and killed and piled the bodies up high. It was like cut bamboo," said Mumtaz, a Rohingya woman from the village of Tula Toli in western Myanmar, who woke up to find herself on a mound of charred bodies.
"In the pile there was someone's neck, someone's head, someone's leg. I was able to come out, I don't know how."
The Myanmar military report attributed the mass exodus of refugees and the repeated reports of military violence to a campaign of misinformation perpetrated by ARSA.
"ARSA Bengali terrorists torched houses and fled to Bangladesh, and were reported to have threatened villagers, saying 'Run away or be attacked by the government troops with launchers, the village will be torched'," the report said.
The Myanmar government does not refer to the Muslim residents of Rakhine State as Rohingya, instead calling them Bengalis, a slur term that implies they are illegal immigrants from Bangladesh.
In their report, the Myanmar government estimated the number of "Bengali terrorists" attacking the military were as high as 10,000 people, although CNN has no way to verify this.
The report said that the refugees "made up news about Myanmar's Tatmadaw committing genocide and ethnic cleansing when international diplomats and media arrived there."
"We've been appalled by the inhumane violence that's taken place in Rakhine State. It's a major humanitarian crisis. It's been created by Burma's military and it looks like ethnic cleansing," the spokesman said, using the traditional name for the country."