Russians in the Far East on Friday scrambled to contain record floods which have affected more than 50,000 people and threatened to paralyse one of the region's biggest cities.

Heavy rains pounding the Far East over the past weeks swelled local rivers, with floodwaters wreaking havoc in Khabarovsk, a city of nearly 600,000 that sits at the confluence of the Amur and Ussury rivers near a Chinese border.

The military were deployed to help hurriedly erect defences against the floodwaters which halted transport in some areas of the city and reached high-rise residential buildings.

Amid fresh concerns that the Russian government was ill-prepared to handle natural disasters, President Vladimir Putin on Thursday said he would soon personally inspect some of the affected areas.

The government will dispatch 10 ministers headed by powerful deputy prime minister Igor Shuvalov to the Far East to oversee relief efforts, government spokeswoman Natalia Timakova told AFP.

On Friday, the level of Amur river, which serves as a natural border with China where it is known as the Heilongjiang river, has risen to 718 centimetres, according to Russian state weather service Rosgidromet.

"The water is still rising, we have not seen the peak yet, and it could climb to 725 centimetres by the end of the day," said Yury Varakin, head of the situation centre at Rosgidromet.

Television footage showed locals walking home along planks to negotiate moody brown waters, junk and discarded footwear floating nearby.

"I went and bought rubber boots, when I came back they were no longer helpful," one man said in televised remarks.

The floods around Khabarovsk are unprecedented since regular monitoring began in 1895, officials said.

The highest water level stood at 642 centimetres in 1897.

There have been no reports of fatalities but officials say the flood waters have so far affected thinly-populated villages and expressed concern that the water might also batter other big cities.

"Right now the floods are reaching big cities which means there could be more serious consequences," the office of the Kremlin's Far Eastern envoy Viktor Ishayev said on Friday.

"The Khabarovsk region has sunk, several districts in Khabarovsk are swimming," Ishayev was quoted as saying on Thursday.

"Komsomolsk-on-Amur has another four to five days to prepare itself for a meeting with big water," he said, referring to a city of 260,000, also on the Amur river.