Some 65,000 Rohingya fled to Bangladesh as the military searched for those behind attacks on police border posts.
Many of those who fled described rapes, killings and other abuses by the army.
But the military said its own investigation found the claims were "false and fabricated".
"Out of 18 accusations included in the [UN human rights body] OHCHR report, 12 were found to be incorrect, with [the] remaining six accusations found to be false and fabricated accusations based on lies and invented statements," Myanmar's state media quoted a report from the military as saying.
The military said it interviewed 3,000 villagers and 184 military officers and troops.
Soldiers were disciplined over two cases, for stealing a motorbike and beating villagers with sticks for failing to put out a fire, the military said.
The crackdown began after insurgents killed nine policemen in attacks on border posts between Myanmar, formerly known as Burma, and Bangladesh in Rakhine state. Reports then emerged that the military were targeting Rohingya indiscriminately.
The UN report in February - compiled from interviews with those who fled the violence - accused the military of abuses including gang-rapes, savage beatings and murder.
It described incidents in which children were killed as their mothers were raped by groups of soldiers, families - including pregnant women and the elderly - being beaten and houses set alight as people sheltered inside.
"The attacks against the Rohingya population in the area... seem to have been widespread as well as systematic, indicating the very likely commission of crimes against humanity," the OHCHR report said.