The girl from the southern province of Kampot died from the H5N1 bird flu virus on Tuesday after suffering from fever, breathing difficulties, diarrhea and other symptoms, the ministry said.
It said the girl and other villagers had shared a meal of chickens that had died.
A 5-year-old girl from the southern Takeo province was also diagnosed with bird flu but is recovering.
The H5N1 virus normally spreads between poultry but can sometimes spread from poultry to humans.
The number of deaths from bird flu in Cambodia this year is the highest since the disease surfaced in 2003. Of the 41 bird flu cases confirmed so far in the country, 30 have been children under age 14.
Minister of Health Mam Bunheng said the spread of bird flu is a particular concern with the approach of the Cambodian festival of Pchum Ben in early October, when families prepare chickens and ducks for meals and offerings.
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