The report has found that three in 10 children, under the age of five years, suffer from diarrhoea which is a major death among kids in the region.
The UN health agency's first ever report on the estimated burden of food-borne diseases underscores the need to take immediate measures to make food safety a public health priority.
The risk of food-borne diseases is the highest in low and middle income settings where hygiene, safe water for preparing food, and adequate food production and storage conditions remain a challenge, WHO regional director for south-east Asia, Poonam Khetrapal Singh, said.
"Food-borne diseases account for a significant proportion of the burden of disease in the region. Diarrhoeal diseases are the leading cause of food-borne disease burden in the region," Singh said citing the report.
Around 55 million children under the age of five fall ill and 32,000 die from diarrhoeal diseases in the south-east Asia region every year, according to the report.
Food contaminated with harmful bacteria, viruses, parasites, toxins and chemicals are the main causes of food-borne diseases.
The deaths and diseases caused by contaminated food can be prevented through improving hygiene, sanitation and other public health measures such as safe drinking water, enforcement of food safety legislation and public awareness and education on safe food handling, the WHO said.
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