The Syrian military has said it shot down a Turkish plane "flying in airspace over Syrian waters", according to state-run news agency Sana.
"[The jet] was dealt with in accordance with the laws that govern such situations," a military spokesman said.
Turkey had earlier said it believed that one of its F-4 fighter jets had been shot down by Syrian forces.
A search for the two crew members is under way, involving Turkish and Syrian coast guard ships.
The F-4 Phantom disappeared over the Mediterranean, south-west of Turkey's Hatay province, near the Syrian coast.
The Turkish military said it lost radio contact with the F-4 while it was flying over Hatay, about 90 minutes after it took off from Erhac airbase in the province of Malatya, to the north-west.
A Syrian military spokesman told Sana that an "unidentified target"" had broached Syrian airspace from a westerly direction at 11:40 local time (08:40 GMT) on Friday.
The target was flying at high speed and at low altitude, the spokesman said.
Anti-aircraft defences had hit the plane with artillery, bringing it down in the sea off the coast of Latakia province, 10km (six miles) from the village of Um al-Tuyour, he added.