The outbreak has struck the far corner of Myanmar's northern Sagaing region, a remote and mountainous area which borders eastern India and is populated by people from the Naga tribes.
The deaths began in June and highlight how vulnerable Myanmar's more isolated populations are in a country where healthcare was never prioritised under decades of brutal and inept junta rule.
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It is one of the many crippling legacies that the newly installed civilian government of Aung San Suu Kyi is trying to tackle.
Than Tun Aung, deputy director general of the disease control department at Myanmar's health ministry, said labwork from the worst hit town of Lahal had come back positive for measles.
"It's measles," he told AFP late Friday. "So we are sending more team members and cooperating with medical doctors from the military as well."
Local Naga representatives had previously accused the central government of being slow to act.
The region is impoverished and very remote, a mountainous border area where roads and electricity are scant.
"It took our first medical team about six days to reach the villages. Communication there is also difficult," Than Tun Aung said.
He said they had confirmed a total of 31 deaths in Lahal region, half of whom were under 15.
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The Council of Naga Affairs gave a higher toll of 39 dead in nine villages with all the deceased children.
Although health budgets slightly increased in the last few years of outright army rule -- which ended with last November's elections -- Myanmar is still one of the lowest spenders in the world on healthcare as a share of GDP.
Last year, with the help of the World Health Organization and the UN, Myanmar embarked on a mass vaccination programme with the aim of eradicating measles and rubella by 2020.
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