He told a special session of the Human Rights Council on the Rohingya on Tuesday: "My government is doing everything possible to deter these extremist acts".
More than 620,000 people have fled into Bangladesh in a matter of months as security forces unleashed a targeted campaign of violence against the Rohingya: killing an unknown number of women, men and children; raping women and girls; laying landmines; and burning entire Rohingya villages.
"Can anyone - can anyone - rule out that elements of genocide may be present?", he told the 47-member state forum in Geneva.
Amnesty International has also documented how Myanmar's security forces are committing wide-ranging violations against other ethnic minorities, in particular in Kachin and northern Shan States.
Bangladesh, which along with Saudi Arabia had requested the special session, meanwhile voiced disappointment that Tuesday's resolution was not adopted by consensus, given the severity of the crisis.
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The resolution calls on Myanmar to "address the root causes" of the Rohingya crisis, and to fully cooperate with the different United Nations bodies, providing full access to investigators and humanitarian workers.
He said that none of the 626,000 Rohingya who have fled to Bangladesh since August should be repatriated unless there was robust monitoring on the ground.
With his government in the spotlight, the ambassador said the priority should be on returning displaced people to Myanmar's Rakhine state.
Htin Lynn said the returnees would be housed in temporary places - but not camps - until arrangements are made to relocate them to their places of origin. It also called for the reform of Myanmar's 1982 Citizenship Law which prevents the Rohingya from becoming citizens though many have lived in the country for generations.
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.
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He noted his office had sent three teams to Bangladesh this year to monitor the situation and interview refugees.
Rights groups welcomed the resolution and called for perpetrators of the violence to be held accountable for their actions.
Myanmar should let investigators into the country to probe alleged atrocities against the Rohingya minority, the UN Human Rights Council demanded Tuesday, as the UN rights chief said that the violations could amount to genocide. "The Myanmar authorities continue to downplay the seriousness of the reports, while refusing to cooperate with the fact-finding mission created by this Council".
"How much do people have to endure before their suffering is acknowledged and their identity and rights are recognised, by their government and by the world?" he asked.
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. "The global community has made clear that it does not accept the denial of both the military and civilian leadership, whose attempts to whitewash these crimes undermine any chance of durable rights or reconciliation". A draft resolution urges Zeid's office to report on cooperation between Myanmar's government with United Nations rights monitors.
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