The deluge has been declared a natural disaster in the worst-affected regions of Amur and Khabarovsk, where Russian President Vladimir Putin called on the army to participate in rescue operations.
Minister of Regional Development Viktor Ishayev said more than 17,000 people had been evacuated and "in the worst-case scenario up to 100,000 people could be evacuated."
In a video conference with regional leaders Putin was quoted by local news agencies as saying: "We should not relax, there is still an enormous amount of work."
He promised that all damaged infrastructure would be repaired, and that while the situation was difficult it was "under control".
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Prime Minister Dmitry Medvedev said 3.2 billion rubles had been put aside for the affected regions, according to the Interfax news agency.
Temporary shelters have been opened up, mostly in schools, to shelter evacuated residents.
Massive rains since the end of July saw the Amur River --
The longest in Siberia which borders northeastern China -- burst its banks, as well as one of its tributaries the Zeya.