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The Health Ministry and the World Health Organisation said in a statement on Wednesday that they are investigating the severe respiratory disease which also has neurological symptoms.
"To date, there is no report of any staff or any neighbouring patients to the cases at the hospitals becoming sick with similar symptoms," it said.
With the investigation still at an early stage, Dr Nima Asgari, a public health specialist for the UN body in Cambodia, said it was difficult to specify the symptoms, which "include high fever and severe chest disease symptoms, plus in some children there were signs of neurological involvement".
Asgari confirmed there was "no cluster of the cases yet" but said the high mortality rate in such a short space of time was worrisome.
"WHO is always concerned about a disease which causes death in such high numbers of children," he told AFP.
The victims, all aged seven and under, were admitted to hospitals in the capital Phnom Penh and the northwestern tourist hub of Siem Reap.