Rescue teams managed to locate one of the pilots on an inflatable raft in the sea after he flashed the emergency signals.
Flights of the Sukhoi Su-34 fighter-bombers have been suspended throughout Russia following an accident in the Far East, a source in the Russian Defense Ministry toldTASS on Monday.
According to some reports one of the two aircraft involved in the collision recovered to a Russian airfield successfully on a single engine following the reported midair collision. "The planes were not equipped with ammunition", the ministry said.
The fate of the second aircraft and its crew is still unknown. The pilot was taken aboard a helicopter, and his condition is described as "satisfactory".
The Su-34, dubbed "Fullback" by North Atlantic Treaty Organisation, is one of Russia's most capable aircraft - able to engage targets on the ground and in the air - and has been used extensively in Syria.
Following a massive search involving several rescue ships and aircraft, two other crewmen were found dead, the ministry said in a statement carried by Russian news agencies. The sole rescued navigator was evacuated to Khabarovsk to receive medical treatment.
According to RIA Novosty, the search party is facing "difficult weather conditions", with a cyclone now on the search area.
The Su-34 is a modern multi-purpose warplane, designed for striking ground targets, aerial combat, and surveillance flights.