"She died midday on April 5. Samples from the girl tested positive for the influenza A/H5N1 virus at the Pasteur Institute of Cambodia in Phnom Penh," they said in a joint statement.
The girl, who was from eastern Kampong Cham province on the border with Vietnam, fell ill with a fever and diarrhoea on Monday and was brought to a local hospital the next day, they said.
The girl was sent to a hospital in the capital Phnom Penh on Wednesday after her condition worsened, the statement said.
It was the first human case of bird flu in Cambodia so far this year, the statement said.
"The Ministry of Agriculture is conducting a detailed investigation into poultry in the area around the village, but it appears that some chickens had been dying in the village before the girl become ill," it said.
A team of investigators from the health ministry, the WHO and the Pasteur Institute have gone to the area to determine whether there were any more cases, the statement added.