Turkey's President, Abdullah Gul, has said the Turkish fighter jet shot down by Syria's air defence forces on Friday may have violated Syrian airspace.
Mr Gul said it was routine for warplanes flying at high speed to cross borders for short distances.
Syria has said it engaged the aircraft in its airspace "according to the laws that govern such situations", and that it crashed into the Mediterranean Sea.
The Turkish and Syrian navies are searching for the two crew members.
Relations between Nato-member Turkey and Syria, once close allies, have deteriorated sharply since the uprising against Syrian President Bashar al-Assad began in March 2011. More than 30,000 Syrian refugees have fled the violence across the border into Turkey.
After a cross-border shooting by Syrian security forces in April that left two refugees dead at a camp near the town of Kilis, Turkey said it would not tolerate any action that it deemed violating its security.
On Saturday, President Gul said the Turkish government could not ignore the fact that Syria had shot down a Turkish aircraft.
"It is not possible to cover over a thing like this, whatever is necessary will be done," he was quoted as saying by state news agency, Anatolia.
"It is routine for jet fighters to sometimes fly in and out over [national] borders... when you consider their speed over the sea," he added.
"These are not ill-intentioned things but happen beyond control due to the jets' speed."
Mr Gul said an investigation would look at whether the plane had been shot down in Turkish airspace, and also revealed that Ankara had been in contact with Damascus despite both countries declaring each other's diplomats unwelcome earlier this year.
"We withdrew our envoy from Syria for security reasons. This does not mean that we have no contacts," he explained.
Deputy Prime Minister Bulent Arinc later said the jet had been on a reconnaissance mission, state television reported.
The BBC's Jonathan Head in Istanbul reports that the Turkish government is treating the loss of the aircraft very seriously, but also with great caution.
Despite public anger over the suffering of civilians in Syria, Ankara has been very reluctant to consider military intervention, our correspondent says.
It will not rush into a military response to this incident either, he adds.
Diplomatic relations between Turkey and Syria have been downgraded to their lowest possible level without completely breaking them.
But the speed with which the coastguards of the two countries organized a joint search-and-rescue operation for the two missing crew members from the plane suggests there are still avenues of communication between their military forces, our correspondent adds.
The Turkish military said it lost radio contact with the F-4 Phantom at 11:58 (08:58 GMT) on Friday while it was flying over Hatay province, about 90 minutes after it took off from Erhac airbase in the province of Malatya, to the north-west.
Later, the Syrian military said an "unidentified air target" had penetrated Syrian airspace from the west at 11:40 local time (08:40 GMT), travelling at very low altitude and at high speed.
It said that in line with the laws prevailing in such cases, Syrian air defences engaged the craft, and scored a direct hit about 1km (0.6 miles) from its coastline.
It burst into flames, and crashed into the sea at a point 10km (6 miles) from the village of Om al-Tuyour, off the coast of Latakia province, well within Syrian territorial waters, the statement added.
Syrian television showed a map charting the aircraft's movements, coming in from over the sea near northern Cyprus.
The military statement said that after it "became clear the target was a Turkish military plane which had entered our airspace", the naval commands of the two countries were in touch, and a joint operation was going on to find the missing crew members.