The death toll from severe flooding in the Black Sea region of southern Russia has risen to at least 150.

Torrential rains dropped more than 28 centimetres of water on the region, flooding more than 5,000 homes.

The water rushed into the area around the hard-hit town of Krimsk in the Krasnodar region with such speed and volume that residents accused local officials of opening a water reservoir in the mountains above.

Federal investigators acknowledged on Sunday that water had been released from the reservoir, but they said it did not cause the flooding.

Local television showed debris scattered across the streets, uprooted trees and overturned vehicles dumped into ditches by the powerful floodwaters.

Speaking on Sunday, Ivan Sengerov, Chief of the Russian Investigative Committee's Krasnodar regional department, said a criminal investigation had been launched to try to determine how rain caused such widespread damage and so many deaths.

Russian President Vladimir Putin flew over the devastation in a helicopter on Saturday.

The interior ministry said Sunday that 150 bodies had been recovered, 139 of them in Krimsk, a town of 57,000 people. Many people were asleep when the flooding hit late on Friday and early Saturday.