"More than 2,000 people, including 405 children, have been evacuated in Primorye," the Russian emergency situations ministry said on Telegram.
The ministry said nearly 5,000 buildings had been flooded in the Primorye region, which borders China and North Korea.
Rescuers had set up 13 temporary accommodation centres in the region, the ministry said.
Flooding in the city of Ussuriysk was the worst in a decade, according to state-run TASS news agency.
Khanun battered Japan earlier this week before taking a circuitous route towards the Korean peninsula.
The storm also forced the evacuation of tens of thousands of scouts from their jamboree campsite in South Korea.
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