The officials handed over the fishermen -- Akiyoshi Kawamura and Haruki Kamiya -- on Wednesday afternoon, said Shunji Yamada, an official in the Japanese Foreign Ministry.
The handover took place after Russian and Japanese officials met aboard a Japanese fisheries patrol boat near Kunashiri Island, Yamada said. The two arrived at Nemuro port on Japan's northernmost main island of Hokkaido later in the day.
"I'm very sorry to have caused a fuss," Kawamura said on a nationally televised news conference.
The captain, Noboru Sakashita, 59, who has reportedly assumed all blame for his boat's purported violation into Russian territory, will remain in Russian custody for the time being, he said.
A Japanese Foreign Ministry spokesman said he welcomed the return of the two fishermen but urged Russia to return Sakashita.
On Aug. 16, a Sakhalin coast guard boat fired at a Japanese vessel off Hokkaido, killing a Japanese crab fisherman. Authorities seized the boat along with its captain and two crew members.
In Moscow, Foreign Minister Sergei Lavrov met with Japanese Deputy Foreign Minister Katsutoshi Kaneda on Wednesday and demanded Japan take measures to ensure Japanese ships stop poaching in Russian waters.
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