The Russian embassy in Pyongyang released a statement saying that the boat Xiangheilin-8, owned by the Northeast Fishery Company based in Nevelsk, Russia, was allowed to set sail from the North Korean port of Wonsan at 7.30 p.m. on Saturday.
The boat headed towards the South Korean port of Sokcho, from where it had departed on July 16 with a crew comprising 15 Russ and two South Koreans.
The South Korean unification ministry confirmed on Sunday that the two South Korean fishermen had returned to Sokcho.
The Russian embassy in Pyongyang said it would continue working to clarify the circumstances surrounding the seizure of the Russian vessel.
According to Pyongyang, the boat was seized on July 17 for "violating the rules of entry and stay in the Democratic People's Republic of Korea".
A statement by South Korean authorities said the 300-ton vessel had set sail from Sokcho, along the eastern coast of South Korea, on July 16.
It was headed for Zarubino, located in Russia's east coast, some 40 km from the North Korean border.
During the voyage, the ship suffered an engine failure and ended up in North Korean waters, Seoul added.
Pyongyang and Moscow share good relations dating back to the founding of North Korea under the Soviet Union's patronage in 1948.
The leaders of both countries, Kim Jong-un and Vladimir Putin, held a summit in Russia's eastern port city of Vladivostok in April, where they vowed to strengthen bilateral ties.
( With inputs from IANS )