While not mentioning the Rohingya directly, Ambassador Htin Lynn says any "dehumanization" of people in Myanmar "could be an act of extremist individuals".
The U.N. estimates over 600,000 Rohingya have fled to Bangladesh since August to escape a bloody crackdown by security forces in Myanmar.
But in his address to Tuesday's special council session, UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein went even further.
During the session, he cited systematic discrimination against Rohingya, policies of segregation, and recent allegations of killings, stabbings, beatings to death, burnings of houses with families inside, rape and sexual abuse, forced displacement, and the systematic destruction of villages, homes, and livelihoods.
He then asked the UN Human Rights Council: "Given all of this, can anyone rule out that elements of genocide may be present?"
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.
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The government of the Buddhist-majority country should not only carry out its plan to repatriate the Rohingya who have fled to Bangladesh, but it should also grant citizenship to the largely stateless and marginalized group.
Zeid said actions by Myanmar's government to "dehumanize" the Rohingya minority were likely to fan more violence and affect more communities across the region.
Marzuki Darusman, who heads the independent fact-finding mission, told the Human Rights Council by videoconference that his team has "not yet come to any conclusion on these issues".
Myanmar disassociated itself from the call for the urgent dispatch of a fact-finding mission, and the government refused to grant entry visas to commission members.
"The council must now step up and pass a strong resolution that sends a clear message to Myanmar's government and military that their abhorrent treatment of the Rohingya must end immediately, and that perpetrators will not enjoy impunity", said James Gomez, Amnesty's regional director for Southeast Asia and the Pacific.
Myanmar's Rohingya minority has "very likely" faced crimes against humanity and possibly genocide at the hands of Myanmar security forces and their helpers, the U.N.'s top human rights body and a top United Nations official said Tuesday.
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Rights advocates hailed the resolution.
"But it needs to ensure that its rhetoric is matched by its will to prevent further mistreatment, forced returns, and assaults to the human rights and dignity of the Rohingya", she said.
"The U.N. resolution makes clear that the worldwide community retains a watchful eye over the plight of the Rohingya and demands action", said Laila Matar, senior U.N. advocate at Human Rights Watch, in a printed statement.
"It is imperative that any individuals or entities responsible for atrocities be held accountable", the U.S. state department said.
Myanmar's military says it is fighting militants and not targeting civilians.
It also asked Zeid's office to track progress in the country and to provide regular updates to the council and submit a full report by March 2019.
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