The plane "identified two bodies, 37 nautical miles to the northwest of Chongjin [in northeast North Korea]" the official said.
Eleven sailors have been found alive from the 18-man crew of the Sinegorye, which sank in the Sea of Japan on Monday, and a total of four have been found dead. The search continues for the other three.
North Korea had given authorization for one South Korean vessel and one plane to enter its waters and airspace on Tuesday, to search for the sailors, despite diplomatic tensions between the countries.
The two Koreas remain technically at war, since no peace treaty was signed following the Korean War in 1953. The so-called Demilitarized Zone between the countries is the most heavily armed border in the world. South Korea has been working toward reconciliation and eventual reunification with its neighbor through its Sunshine Policy, but tensions between the countries escalated recently over North Korea's controversial nuclear test.
Russia also shares a short border with the reclusive Communist state.
North Korean military officials were quoted by South Korean coast guards as saying "Guided by humanitarian considerations, our side has decided to allow the rescue teams to enter our territory, aboard one ship and one plane."
The Sinegorye, which was transporting timber, sunk within one hour when a sudden heavy storm broke out, causing the vessel to lurch violently. Most of the timber broke through the holds, damaging hatches and equipment, and water began to flow into the ship, one of the survivors, speaking from a South Korean hospital, said.
Russia's Foreign Ministry said Tuesday it had instructed its Pyongyang embassy to make every effort jointly with local authorities to locate and rescue the remaining crewmembers.
