Mainly Buddhist Myanmar denies the Muslim Rohingya are its citizens and considers them foreigners.
But the United Nations human rights chief, Zeid Ra'ad al-Hussein, challenged the council, insisting that the possibility of genocide was real.
China, the Philippines and Burundi voted against the measure.
The United Nations human rights chief, Zeid Ra'ad al-Hussein, said in Geneva on Tuesday that Burmese security forces may be guilty of genocide, adding global pressure on Myanmar to be investigated for crimes against humanity.
Rohingya refugees continue to flee Myanmar for Bangladesh even though both countries set up a timetable last month to allow them to start to return home, the United Nations refugee agency (UNHCR) said on Thursday.
Myanmar's representative at the meeting continued to reject accusations of atrocities, saying refugees accounts are made up or forced.
More than 600,000 Rohingya fled to Bangladesh after the Myanmar security forces launched a brutal offensive targeting the minority in the Rakhine state in late August.
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". They include indiscriminate shooting and stabbing of villagers, rape, beatings and the burning of houses with families inside. Zeid Raad al-Hussein asked the UN's Human Rights Council at a meeting in Geneva, Switzerland overnight, ABC News reported.
But Zeid told the council: "Considering Rohingyas' self-identify as a distinct ethnic group with their own language and culture - and [that they] are also deemed by the perpetrators themselves as belonging to a different ethnic, national, racial or religious group - given all of this, can anyone rule out that elements of genocide may be present?"
The U.N. human rights chief says actions by Myanmar's government to "dehumanize" the Rohingya minority are likely to fan more violence and draw in communities from across the region.
He was speaking at a special council session Tuesday on the Rohingya's plight.
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