The decision and the health concerns were blows to its owner, Italian confectionery giant Ferrero, coming at the height of the Easter holiday season when its Kinder chocolates are sought-after supermarket buys.
Ferrero issued a statement saying it "sincerely apologises" for the spate of salmonella cases and acknowledging the suspension of operations of its factory located in the southeastern town of Arlon.
Belgium's food safety authority, AFSCA, said in a statement the plant was ordered shut "following the findings of the last few hours that information provided by Ferrero is incomplete".
It ordered the recall of the factory's entire production of the company's popular Kinder brand.
The authority "will only authorise the reopening of the site once it has been concluded that the establishment complies with all food safety rules and requirements," it added.
Belgian Agriculture Minister David Clarinval said that "such a decision is never taken lightly, but the current circumstances make it necessary. The food security of our citizens can never be neglected."
Ferrero said it "acknowledges there were internal inefficiencies, creating delays in retrieving and sharing information in a timely manner".
"With immediate effect" the factory's entire production of Kinder Surprise, Kinder Mini Eggs, Kinder Surprise Maxi 100g and Kinder Schoko-Bons was halted, it said.
"We deeply regret this matter. We want to sincerely apologise to all our consumers and business partners and thank the food safety authorities for their valuable guidance," Ferrero said.
The company, which also makes Nutella and Tic Tac candies, on Thursday recalled certain varieties of its Kinder chocolates in the United States which had been made in Belgium.
That followed recalls earlier this week in the United Kingdom and several European countries over concerns about products from the factory.
Salmonella is a type of bacteria that can cause symptoms including diarrhoea, fever and stomach cramps in humans, and is one of the most common food-borne infections.
Most cases are caused by the ingestion of food contaminated with animal or human faeces.
Britain's Food Standards Agency has said 63 cases of salmonella have been identified across the UK.
In France, at least 21 cases have been reported and 15 reported having eaten Kinder products that have now been recalled, according to the French public health service.
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