The junta's foreign ministry said the report was based on "sweeping allegations against the government and its security forces", in a statement on its Facebook page on Tuesday.
"Myanmar, therefore, asserts its firm objection against the irrelevant recommendations made by the High Commissioner."
The junta acknowledged that the UN report recognised the violence committed by some of the groups arrayed against it, but only "slightly".
Swathes of the country are in turmoil, and killings of low-level junta officials and anti-coup fighters take place almost daily, with details murky and reprisals often following quickly.
The junta claims more than 5,000 civilians have been killed by "terrorist" groups since the coup.
Diplomatic efforts to resolve the bloody impasse led by the UN and the Association of Southeast Asian Nations regional bloc have made little headway, with the generals refusing to engage with opponents.
The UN Security Council passed its first resolution on the situation in Myanmar in December, urging the junta to release Suu Kyi and all "arbitrarily detained prisoners".
Security Council permanent members China and Russia abstained, opting not to wield vetoes following amendments to the wording.
India, which has close ties with the junta, also abstained.
More than 3,000 people have been killed in the military's crackdown on dissent according to a local monitoring group.