The NATO member is home to opposition forces fighting Syrian President Bashar Assad and has called for the removal of Assad to help defuse the crisis in the neighboring Arab country.
There was no immediate official confirmation of Turkish media reports the F-4 was shot down Friday by Syrian security forces over the Mediterranean Sea but the military said both pilots were safe.
Turkish Prime Minister Recep Tayyip Erdogan, quoted in the media said, "the other side have expressed regret."
There was no word from Damascus about the incident.
Turkey is NATO's eastern most neighbor and helped with NATO military operations last year that brought down Libyan leader Moammar Gadhafi.
Turkey's military role in Syria has been low key but that is seen changing rapidly with the armed opposition carrying operations inside Syria.
Relations between Turkey and Syria, once close allies, have been deteriorating since the uprising against Syrian government began in March 2011 and anti-Assad opposition forces began gathering in Turkey.
A Turkish military statement said authorities lost radio contact with the F-4 Friday while it was flying over Hatay, about 90 minutes after it took off from Turkey's Erhac Airbase in the Malatya province.
Turkish media broadcasts cited military sources who denied the jet had entered Syrian airspace and gave details of how Turkish and Syrian coast guards collaborated to recover the pilots.
Reports quoting unnamed witnessed who said they saw the plane shot down by Syrian forces couldn't be confirmed by officials.
U.S. commentator Morton Abramowitz, in a commentary on Turkey, said Erdogan might be at risk of losing direction after a successful period with a buoyant economy and expanding influence in the Middle East.
Abramowitz, a senior fellow at The Century Foundation, which has offices in New York and Washington, wrote in the commentary, syndicated on the Internet, the Turkish leader was at risk of misjudging the situation and undermining Turkish interests.
Abramowitz called Syria "Erdogan's biggest disaster," which had also landed Turkey with the problem of having to take care of rising numbers of Syrian refugees. About 26,000 Syrians have fled the conflict and sought refuge in Turkey.
Analysts say Turkey appears increasingly at risk of getting dragged into a wider regional conflict because of its deteriorating ties not only with Assad but also with Iraq and traditional friend Iran. Turkey's ties with Israel became strained after the May 31, 2010, Israeli commando raid on a Turkish-led pro-Palestinian relief flotilla that left nine activists dead and scores wounded on both sides.