Rescuers attempt to save people from thousands of flooded homes in Russia's Krasnodar region near the Black Sea. Reuters

Torrential rains dropped nearly a foot of water in the Black Sea region of Krasnodar, southern Russia, overnight, causing heavy flooding that killed at least 103 people and forced many to flee for refuge in trees and on roofs.

Muddy water coursed through streets and homes in the hard-hit town of Krimsk, about 750 miles south of Moscow, where at least 67 people died. The flood water was high enough to flow over the bonnets of cars and to reach some rooftops, according to witnesses.

People waded through waist-high water or manoeuvred through the streets in boats on Saturday. About 5,000 residences were flooded, the Krasnodar governor told the Interfax news agency.

"Nobody remembers such a flood in all [of the area's] history," Alexander Tkachev said.

The interior ministry gave the death toll as 103. Five people died of electric shocks in the Black Sea coastal city of Gelendzhik after a transformer fell into the water, the state news agency, RIA Novosti, said.

Anna Kovalevskaya, whose parents live in the flooded area, described water indundating their home up to the roof.

"In the town people are saying that a reservoir in the mountains above was opened," she told the Moscow-based radio station Russian News Service. "A wave came from there. There was seven meters (22 feet) of water in the town."

The state news channel, Rossiya 24, showed video of residents rescuing people in small inflatable boats and others slogging glumly through flooded homes.

"It came so fast!" exclaimed one woman, whose name was not given, waving an arm in frustration at the shin-deep water in her living room, where a large teddy bear sat on a sofa.

As of 10am on Saturday, more than 28cm (11 inches) of rain had fallen in Gelendzhik since Friday evening, the state meteorological service said.

Gelendzhik is a popular summer holiday spot on the Black Sea coast. The Russian deputy prime minister Olga Golodets told RIA Novosti that 7,100 children were at holiday camps in the area, and that 459 children had to be evacuated.

The area also includes Novorossiisk, a major Black Sea port. The Transneft oil company said it had suspended loading oil on to tankers at the port because of the severe weather.

More than 1,500 emergency ministry officials were working to aid flood victims and clean up the damage, state TV said.