With winds packing speeds of more than 70 kilometres (43 miles) an hour, the weekend storm unleashed violent torrents of mud and water with floods reaching 1.5 metres (five feet) in some areas.
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"A child aged 12, whose disappearance was reported yesterday (Monday) afternoon, has unfortunately been found dead in the mud by his father," police spokesperson Natalija Spirova Kordic told AFP.
"In addition, a 16-month-old baby is missing. He was in a car with his father, who drowned in the vehicle," she added.
Skopje and the northwestern city of Tetovo, where heavy storms caused damage to property but no casualties, remain under a state of emergency.
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Villages on the northern outskirts of the capital were particularly badly affected.
Macedonia's weather service said 93 litres of water per square metre fell in two hours on Skopje -- equivalent to the average for an entire month of August.
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