The WHO and Cambodia's Ministry of Health said in a joint statement Thursday that an investigation had focused on 61 children, 54 of whom have died.
A majority of 31 samples collected from patients tested positive for a virus that causes the illness, a common infectious disease that is most serious among children, the statement said.
Most of those affected were under the age of 3.
"The Ministry (of Health) are starting their surveillance to look at identifying severe cases," said Nima Asgari, WHO public health specialist. Asgari said health authorities would also examine mild cases of hand, foot and mouth disease in health centres.
The WHO issued a global alert last week about the illness, whose symptoms include high fever, respiratory and neurologic symptoms, and rapid deterioration of respiratory functions.//DPA