The fate of the other 15 crew of the 2,448-tonne Sinegorye, sailing from Russia's Far East to China and carrying timber, was unknown.
The South Korean coast guard said the Sinegorye sent a mayday call at around noon on Monday about 70 miles (110 km) off Ullung Island on the east coast and was believed to have sunk. Water had entered its cargo compartment in rough seas.
The three crew were found by a South Korean ship helping in the search.
"A life raft with one crewman, who was alive, was found. Another two were pulled from the water, also alive," Interfax quoted a Russian rescue service official as saying.
"The Sinegorye's lifeboat has also been found but there was no one in it," the official said.
Two large patrol boats and a search aircraft were dispatched to the area but the ships experienced difficulty reaching the area until well into the night, a South Korean coast guard official said by telephone from the coastal city of Donghae.
"It is too early to talk about the fate of the (other) crew members," the official said. "Weather conditions remain extremely bad."
Torrential rain hit South Korea's northeastern region on Monday.

Copyright Reuters, 2006