Moscow declared a federal emergency on Sunday over floods in the Orenburg region, where the Ural river left much of the city of Orsk covered in water, forcing thousands to leave their homes.
The river is now reaching dangerous levels in the regional capital of Orenburg, a city of 550,000 people.
The Kremlin has also warned of "inevitable" floods in western Siberia's Kurgan and Tyumen regions.
Thousands of people have already been evacuated from flooded areas.
The Kremlin said on Monday that over 10,000 residential buildings had been flooded, mostly in the Urals, Volga area and western Siberia.
Emergency services warned of a "rise in air temperature, active snow melting and the overflow of rivers".
Much of the city of Orsk was under water after torrential rain caused a nearby dam to burst.
Orenburg region authorities said that while the Ural river "went down by nine centimetres (3.5 inches)" in Orsk, water levels in the city of Orenburg were rising fast.
"In Orenburg, in a day there was a rise by 16 centimetres to 872 centimetres," in the water level, the regional government said.
Its mayor, Sergei Salmin, told Russian television that the city "has not seen so much water" in decades.
"The highest (water) mark was in 1942. That was 946 centimetres," Salmin said.
"Since then there have been no floods. This is unprecedented."
The Kremlin has said President Vladimir Putin is being briefed on areas affected by "nature anomalies" in real time.
On Monday, it said Putin ordered a government commission to be established on the floods.
- 'No time for convincing' -
Orenburg mayor Salmin said authorities had evacuated 736 people in the city, as they expect the water to rise further.
Over the weekend he warned of forced evacuations if people did not cooperate, saying: "There is no time for convincing."
Russia's weather monitor Rosgidromet said it did not expect the flood in Orenburg to peak until Wednesday and warned that many districts of the city would be affected.
The Ural river flows through Orenburg and into Kazakhstan, where President Kassym-Jomart Tokayev said the floods were one of the worst natural disasters to affect the area in decades.
After evacuating over 6,000 people in the Orenburg region, authorities also began relocating some residents of the Siberian city of Kurgan, where the Tobol river is expected to rise.
Kurgan is a city of around 300,000 people near northern Kazakhstan.
Emergency services in Kurgan said 571 people were moved away from areas expected to be flooded in what it said were "preventative evacuations".
Local authorities said reinforcements of some 100 rescuers arrived in the western Siberian region from the Urals to prepare for the floods.
Emergency authorities also warned that the Irtysh river was "very likely" to flood parts of Tobolsk, one of Russia's oldest Siberian cities.
Putin, who has been a vocal climate sceptic for much of his rule, has in recent years ordered his government to do more to prepare Russia for extreme weather events.
The country has seen severe floods and fires in recent springs and summers.
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