Rights envoy Yanghee Lee made the appeal in a report submitted to the UN rights council, currently holding its main annual session in Geneva.
She urged the 47-member body to establish a COI "to investigate the systematic, structural, and institutional discrimination in policy, law and practice, as well long-standing persecution, against the Rohingya and other minorities in Rakhine State."
She said the probe should focus on violence in 2012, 2014 and the army crackdown on Rohingya Muslims in northern Rakhine since October, which came in retaliation for attacks by militants on police border posts.
A UN rights office investigation accused Myanmar's security forces of murder, rape and torture in the Rakhine operation since October.
Myanmar has dismissed mounting international pressure over alleged abuses of Rohingya Muslims as "biased and unfair".
Escapees have given the UN chilling accounts of babies being stabbed to death, people being burnt alive and widespread gang rape during those operations.
Setting up a COI must be done through a resolution approved by council members, which could be adopted before the session ends later this month.
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