"Can anyone — can anyone — rule out that elements of genocide may be present?" Zeid Ra'ad Al-Hussein asked the UN's Human Rights Council at a meeting in Geneva, Switzerland on Tuesday.
He cited a long list of atrocities Rohingya who have fled to Bangladesh say they have suffered, describing them as "acts of appalling barbarity".
"[They include] deliberately burning people to death inside their homes, murders of children and adults, indiscriminate shooting of fleeing civilians, widespread rapes of women and girls, and the burning and destruction of houses, schools, markets and mosques," he said.
Mr Zeid Al-Hussein had previously described the campaign by Myanmar's military as "textbook" ethnic cleansing.
However, while ethnic cleansing is not a designated offence under international law, genocide is the most serious of atrocity crimes.
Mr Zeid Al-Hussein urged the UN to set up a new mechanism to allow criminal prosecutions of individuals suspected responsible, ABC News reported.
The call for a new approach to prosecutions reflects the dim prospect of charges through the International Criminal Court.
Myanmar does not accept its jurisdiction, meaning the Security Council's unanimous support would be needed to force an investigation.
But it is considered highly unlikely that China, a major investor and trading partner for Myanmar, would agree.
Myanmar continues to bar UN investigators from the country, and Mr Zeid Al-Hussein acknowledged that prosecutions for such crimes were "rare".
Myanmar's representative at the meeting continued to reject accusations of atrocities, saying refugees accounts are made up or forced.
Mainly Buddhist Myanmar denies the Muslim Rohingya are its citizens and considers them foreigners.
However, it says it is working to implement a deal to allow the return of the 620,000 Rohingya who have fled to Bangladesh over the past three months.
Meanwhile, another Myanmar official has reportedly denied plans to hold any returning Rohingya in camps, following earlier reports that authorities were building large detention facilities for them.
In the sprawling camps of southern Bangladesh, now home to over 800,000 Rohingya, many say they would prefer to remain there, because they do not trust Myanmar's assurances of safe return.