Around 740,000 Rohingya fled over the border into Bangladesh after a bloody military campaign in 2017.
The UN condemned the crackdown as ethnic cleansing and investigators called for top military leaders, including Senior General Min Aung Hlaing, to be prosecuted for genocide.
But the military has maintained its operations were justified to root out Rohingya insurgents following a series of deadly attacks on police posts and has denied nearly all allegations of wrongdoing.
In an interview Japan's Asahi Shimbun newspaper published Friday, Min Aung Hlaing doubled down on previous claims, arguing "there is no certain proof that the national army was involved in the persecution" of Rohingya.
The army chief added that accusations the military committed atrocities "hurts the nation's dignity".
Min Aung Hlaing rarely speaks to the press and has instead preferred to communicate over Facebook, but the social media giant kicked him off the platform last year for his role in stoking hate speech.
His comments were at odds with testimony from Rohingya in the crowded, sprawling camps in Bangladesh.
The refugees have recounted widespread murder, rape, torture and the burning of entire villages to the ground at the hands of Myanmar soldiers.
A UN probe report released in September also outlined atrocities committed by the military in meticulous and searing detail.
It said Myanmar's "clearance operations" were disproportionate to the insurgent attacks and cited prior troop deployments as evidence of premeditation.
Investigators called for Myanmar to be referred to the International Criminal Court (ICC) but any road to prosecution would be long and fraught with political difficulties at the UN.
Aung San Suu Kyi's civilian government remains in a fragile power-sharing agreement with the military, which holds three key ministries and a quarter of parliamentary seats.
Suu Kyi's international reputation lies in tatters for refusing to stand up for the Rohingya.
In Myanmar, the Rohingya are widely seen as interlopers from Bangladesh and have been denied citizenship, rights and access to services for decades under what Amnesty International calls apartheid-like conditions.