Flash floods deluged Russia's southern Krasnodar, killing at least 134 people in the region's worst natural disaster in decades, officials and witnesses said Saturday.

President Vladimir Putin inspected the damage by helicopter and held a brief meeting with local officials in Krymsk amid recriminations from residents who accused the authorities of abandoning them.

Television footage showed torrents of brown flood water gushing along streets in the worst-hit town of Krymsk past blanket-covered bodies.

Residents were caught by surprise by the sheer force of the waters, which ripped up pavements and traffic lights and flooded buildings.

In Krymsk, some people woke in the middle of the night to find water pouring in, trapping them in their homes. One woman had to spend the night up a tree before being rescued.

Authorities estimated that up to 13,000 people had been affected in the Krymsk district.

"Our house was flooded to the ceiling, we could not open the door because of the water, so we broke the window to climb out," Krymsk pensioner Lidiya Polinina told AFP by telephone.

"I put my five-year-old grandson on the roof of our submerged car, and then we somehow climbed up into the attic. I don't know how we managed to survive," she said, adding that they had received no warning or assistance.

"It was like a tsunami!" Putin commented as he was told about the flood by local officials, promising to rebuild the ruined properties.

State television footage showed him speaking with emergency ministry officials, who assured him the flood was not caused by problems at a nearby dam, as alleged by locals.

Officials said at least 123 of the bodies had been recovered in the Krymsk area, including a 10-year-old child, but were unable to explain the scale of the toll there, saying the floods were caused by torrential rains.

Polinina said her elderly neighbour had died after becoming trapped by the flood waters.

"She was paralysed. She couldn't get out of the house," she told AFP.

"Everything has been destroyed," she added. "We need help pumping water out of the house, we have no drinking water."

The town, which has a population of 57,000, lies about 200 kilometres (125 miles) northwest of the Black Sea resort town of Sochi where Russia is hosting the Summer Olympic Games in 2014.

Krymsk was still without power on Saturday. Water marks indicated that the water rose as high as seven metres (22 feet).

Officials said the disaster struck as residents slept after the level of the local Bakanka river rose overnight Friday to Saturday.

"Everything happened at night and very quickly," the regional administration said in a statement.

The Russian Internet was meanwhile abuzz with speculation that the flooding was a man-made catastrophe resulting from the opening of a sluice gate at a mountain reservoir. Authorities denied the reports.

A regional environmental group Environmental Watch on North Caucasus said the level of damage on the ground indicated that the rush of water originated at the dam on the local Naberdzhai river, but could not provide details.

Krasnodar region governor Alexander Tkachev called the theory "nonsensical" and appealed to his Twitter audience to stop spreading "stupid" rumours.

"Some opponents, the opposition, are trying to tell some tales," Tkachev complained to Putin at the meeting in Krymsk, assuring that the dam "is functioning normally."

A Krymsk resident who gave her name as Tatyana told AFP by telephone the disaster struck unexpectedly.

"The water rose very quickly.... It flooded people's ground floors in five to 10 minutes, ripped out pavement kerbs and even pieces of asphalt," she said.

Locals had received no warning from the emergency services, she added.

The resort town of Gelendzhik received five months' worth of rain in 24 hours, the regional administration said.

Russian Railways said it had to suspend train traffic due to "difficult weather conditions" in the area, delaying dozens of trains.

Novorossiisk saw two months' worth of rain in 24 hours.

A team had worked through the night to bring the situation under control at the port, port spokesman Mikhail Sidorov said.

The floods had affected the port's operations and pipeline operator Transneft had informed management that it would halt shipments of crude oil, he added.

Krasnodar regional police said they went on high alert at nightfall to "patrol the streets and protect people's property from looters".