It is believed to be the most serious storm to hit Moscow in more than 100 years.
"The hurricane was unprecedented for Moscow," TASS news agency quoted him as saying.
News agencies reported falling trees had blocked roads and metro railways.
An elderly man was killed while waiting at a bus stop and two more died when a tree fell onto their summer house.
Moscow is usually spared such extreme weather, though high winds are not unusual in the region in the summer months.
The death toll was the highest due to storms in the capital in a single day for almost 20 years. Between eight and 11 people died in a storm in the capital in 1998.