Turkey said Saturday its downed fighter jet may have violated Syrian airspace after Damascus confirmed shooting it down, sparking a fresh crisis amid nosediving ties between the erstwhile allies.

President Abdullah Gul said it was routine for warplanes flying at high speed to cross borders, in comments that showed signs of easing tensions in the spat over the shooting in the eastern Mediterranean.

"It is routine for jet fighters to sometimes fly in and out over (national) borders ... when you consider their speed over the sea," Gul told reporters, stressing that such actions were not "ill-intentioned."

Turkey was considering its response after Damascus confirmed it had on Friday shot down the Turkish jet it said had entered its territory, and both countries were searching for the two missing pilots.

"An unidentified aerial target violated Syrian airspace, coming from the west at a very low altitude and at high speed over territorial waters" in the eastern Mediterranean, a military spokesman told Syria's official SANA news agency.

Anti-aircraft batteries had opened fire, hitting the plane as it was one kilometre away from land and it crashed about 10 kilometres (six miles) off the coast of Latakia province in Syrian territorial waters, he added.

It had been subsequently established that the plane was a Turkish fighter jet and the two countries' navies were now cooperating in an operation to find the two missing pilots, SANA reported.

Turkish Prime Minister Recep Tayyip Erdogan said after a top security meeting after the incident that Ankara "will announce its final position and take necessary steps with determination after the incident is entirely clarified."

The incident will further test relations between the two neighbours, already strained over Erdogan's outspoken condemnation of Syria's bloody crackdown on protests against the government of President Bashar al-Assad.

A spokesman for the UN Secretary General Ban Ki-moon said he was following the situation closely.

"He hopes this serious incident can be handled with restraint by both sides through diplomatic channels," said Martin Nesirky.

The military plane vanished off radar screens around 0900 GMT Friday after it took off from an airbase in Malatya city in Turkey's southeast.

President Gul said contacts were established with Damascus although Ankara had withdrawn diplomats from its Damascus embassy and expelled Syrian diplomats after the escalating violence in Syria.

"We withdrew our envoy from Syria for security reasons. This does not mean that we have no contacts (with Damascus)," he said.

Erdogan's government broke with Damascus regime after his former ally Assad launched a deadly crackdown on popular revolts that erupted mid-March last year.

Syrian activists say the violence has cost more than 15,000 lives.

Turkey has now taken in more than 30,000 civilians who fled the violence in Syria, housing them in camps near the border, according to foreign ministry figures.

The country is also playing host to army defectors, including 12 generals. But this incident is the most serious one yet between the two countries.

"If it is interpreted as an assault on Turkey, the debate over whether to invoke the Article 5 of NATO treaty could resurface," professor Huseyin Bagci told the private NTV television channel.

Bagci was referring to the clause which stipulates that an attack against a member of the North Atlantic Treaty Organisation is considered an attack on all members of the alliance.

Turkey has already considered invoking the NATO article after ricocheting bullets fired on the Syrian side of their common border killed two Syrians on Turkish soil in April.

"The question that needs to be asked here is if Syria shot down the plane out of animosity against Turkey," commented Serkan Demirtas, Ankara bureau chief of the English-language Hurriyet Daily News.

"The answer will determine Ankara's approach toward Damascus," he said.

"Assad is playing with fire," headlined mass-circulation daily Hurriyet, while Vatan newspaper said: "They (Syria) will pay the price."

Also Friday, Ankara denied allegations in a New York Times report that cited US officials and Arab intelligence sources to say that Turkey was among a number of countries shipping weapons to Syrian rebels across the border.