"As of 11.00 this morning (IST), we have discovered 15 victims (of the storms). Our teams are still searching for other possible victims," police spokeswoman Liza Bendevska told AFP.
Six people were missing, according to the police, while media reported that about one hundred others suffered injuries, most of them minor.
Among the dead was an eight-year-old girl, a hospital source told AFP.
"This is a disaster, we have never experienced such a thing," said Skopje's Mayor Koce Trajanovski.
The freak weather included winds blowing at more than 70 kilometres (43 miles) an hour and resulted in flash floods and landslides, local media reported.
Cars were seen swept away by the torrents, testifying to the force of the storm.
Especially badly hit were villages on the outskirts of the capital including Smilkovci, Singelic, Stajkovci and Aracinovo.
Reports said the water level reached as high as 1.5 metres (five feet) in some of the affected areas, which were being combed by Macedonia's police and army for survivors and other victims.
Macedonia's hydrometeorological service said 93 litres per square metre fell in two hours on Skopje- equivalent to the average for an entire month of August.
Municipal authorities urged people to avoid going out in the streets, especially driving, with several roads of the capital still flooded and traffic interrupted on the city's ring road.
Violent storms also battered the northwestern city of Tetovo causing property damage but no casualties, while severe thunderstorms also affected the holiday spot of Lake Ohrid in the southwest.
In the spring of 2014, the Balkans region was hit by its worst floods in more than a century, which left 47 people dead in Serbia and Bosnia.
A total of 1.6 million people were affected.
The forecast for today showed unsettled weather in landlocked Macedonia, with possible new showers and strong winds.
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