Fierce storms packing strong winds and torrential rains overnight killed at least 20 people in Macedonia's capital of Skopje, the health minister said Sunday.

The freak weather included winds blowing at more than 70 kilometres (43 miles) an hour and resulted in flash floods and landslides, with cars swept away by the violent torrents.

Weather officials said the average rainfall for the whole of August fell on Skopje in the space of just two hours.

"Unfortunately, 20 people have died," said Health Minister Nikola Todorov, who is coordinating rescue operations.

Local media reported that about 100 others suffered injuries, most of them minor, while a hospital source told AFP that an eight-year-old girl was among the dead.

An emergency was declared in Skopje and certain parts of the northwestern city of Tetovo, where heavy storms caused property damage but no casualties.

"This is a disaster, we have never experienced such a thing," said Skopje's Mayor Koce Trajanovski.

Rain began falling at 5:30 pm (1530 GMT) on Saturday and stopped only around 9:30 on Sunday morning, with the peak of the storm in the middle of the night, around 3:30 am.

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.

Especially badly hit were villages on the outskirts of the capital including Smilkovci, Singelic, Stajkovci and Aracinovo.

"Everything was a mess. Televisions, the fridge, the sofa, everything was floating... it was a nightmare," said Baze Spriovski, a 43-year-old in Singelic, who remained without electricity.

- 'Really horrific' -

Macedonia's weather service said 93 litres per square metre fell in two hours on Skopje -- equivalent to the average for an entire month of August.

Meteorologists said more than 800 lightning strikes were recorded in the first two hours of the storm, which went on for about five hours in total.

"There were thunderbolts with lightning almost every second. It was really horrific," said Biljana Joneska, 62, in Skopje.

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.

Severe thunderstorms also affected the holiday spot of Lake Ohrid in the southwest.

Skopje previously suffered disastrous flooding in 1962, a year before a huge earthquake that almost destroyed the city.

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 Sunday showed unsettled weather in landlocked Macedonia, with possible new showers and strong winds.