An army chief in the provincial capital of Jayapura, Boni Christian Pardede, said 25 people in one subdistrict had died from malnutrition and an outbreak of diarrhea.
He said the situation in mountainous Okbab subdistrict was first reported last week by church activists, who said 23 children and four adults had died. However, Pardede said the latest reports from a health team who had arrived there put the death toll at 25.
Meanwhile, a health official in remote Asmat district said the death toll from a measles outbreak and malnutrition since September has risen to 70 people.
The latest two victims were children who died Saturday in the state-run hospital in Agats, the main town of Asmat.
Papua and neighboring West Papua are the poorest provinces in Indonesia and home to a decades-old independence movement and armed insurgency.
The region is culturally and ethnically distinct from the rest of Indonesia, which annexed it in the early 1960s.
The Indonesian military sent a team of more than 50 doctors and paramedics last week to assist in the response to the measles outbreak.
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