Turkey's President, Abdullah Gul, says the Turkish fighter jet shot down by Syria's air defence forces may have violated Syrian airspace.
Mr Gul says it is routine for warplanes flying at high speed to cross borders for short distances.
Syria says it engaged the aircraft in its airspace according to the laws that govern such situations, and it crashed into the Mediterranean Sea.
Meanwhile the Turkish and Syrian navies are searching for the two missing crew members.
The Syrian military has admitted shooting down the F4 Phantom fighter jet, saying it was flying in airspace over Syrian waters.
The F-4 Phantom disappeared over the Mediterranean, south-west of Hatay province, near the Syrian coast at 11.58am on Friday.
Turkish prime minister Recep Tayyip Erdogan has held a two-hour emergency meeting with his interior, defence and foreign ministers and the Chief of the General Staff.
Mr Erdogan's office says Turkey will respond decisively once all the circumstances are established.
Anti-aircraft defences hit the aircraft, bringing it down in the sea off the coast of Latakia province, a Syrian military spokesperson said.
It later became clear the target was a Turkish military plane which had entered our airspace, he continued.
It was dealt with in accordance with the laws that govern such situations, he said.
However, a BBC correspondent says Turkey is not likely to do anything beyond demanding an apology from Syria.
Relations between Turkey and Syria, who were once close allies, have deteriorated sharply since an uprising against President Bashar al-Assad began in March 2011.
Thousands of Syrian refugees have since crossed the border into Turkey.
NTV earlier reported the Syrian coast guard was helping the Turkish coast guard, navy and air force search for the plane and its two crew.
Russian Foreign Minister Sergei Lavrov has been quoted in St Petersburg by the Interfax agency as saying that a cargo ship that turned back toward Russia while travelling to Syria, was carrying three repaired helicopters and air defence systems.
The ship returned to Russia after British officials contacted its insurer and persuaded the company to cancel the vessel's cover.
The European Union has an arms embargo on Syria.
The ship was thought to be carrying attack helicopters to Syria for use against anti-regime protestors.