Syria confirmed on Saturday that it shot down a Turkish warplane over its territory, sparking a fresh crisis on the two countries' long border which is already awash with refugees and rebel fighters.

Prime Minister Recep Tayyip Erdogan said NATO member Turkey would take all necessary steps once it had established the facts of Syria's downing of the F-4 fighter jet in Mediterranean waters on Friday.

Tensions between the two neighbours were already running high as Ankara has taken a tough line on Damascus's bloody crackdown on a 15-month-old uprising against the rule of President Bashar al-Assad, giving sanctuary to defecting military personnel who have formed the kernel of an expanding rebel army.

Syria's official SANA news agency confirmed that Damascus had downed the jet in a terse report early on Saturday.

"An unidentified aerial target violated Syrian air space, coming from the west at a very low altitude and at high speed over territorial waters," the news agency quoted a military spokesman as saying.

Anti-aircraft batteries opened fire, hitting the plane as it was one kilometre (less than a mile) from land, the spokesman said.

It crashed about 10 kilometres (six miles) off the coast of Latakia province in Syrian territorial waters, he added.

The two countries' navies were now cooperating in the search for the two missing air crew, SANA reported.

The Turkish prime minister convened an emergency meeting of military and intelligence chiefs and key ministers soon after contact was lost with the plane on Friday.

"Turkey will announce its final position and take necessary steps with determination after the incident is entirely clarified," Erdogan said after the meeting.

Erdogan's government broke with the Damascus regime after his former ally Assad launched a deadly crackdown on mass protests that erupted in March last year.

Turkey has hosted several meetings of the exiled Syrian opposition aimed at forming a united front against the Assad regime and has opened its borders to an exodus of refugees fleeing the crackdown.

Turkey is a key member of NATO, whose charter stipulates that an attack against any member of the Western military alliance is considered an attack on all.

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

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

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 downing of the plane comes amid a flurry of reports in the Western media that rebel fighters active in northern provinces of Syria are receiving weapons chanelled from the Turkish side of the border.

Britain's Guardian newspaper reported on Saturday that Turkey has allowed a command centre to be set up in Istanbul to coordinate the supply of weapons.

"The centre is believed to be staffed by up to 22 people, most of them Syrian nationals," the Guardian reported.

The paper said one of its journalists had witnessed weapons transfers near the border earlier this month.

The Guardian's report came after a strong denial by Ankara on Friday of a similar report by the New York Times.

"Turkey does not ship weapons to any neighbouring country, including Syria," foreign ministry spokesman Selcuk Unal said.

The New York Times had reported that US intelligence operatives in Turkey were vetting the flow of weapons to Syrian rebels to ensure they do not fall into the hands of Al-Qaeda militants.

It cited unnamed US officials and Arab intelligence officials as saying the weapons were being paid for by Turkey, Saudi Arabia and Qatar and taken across the border by a shadowy opposition network.

Unal acknowledged on Friday that Turkey was sheltering 12 Syrian generals who had defected to join rebel ranks. He said they were among 32,750 Syrian refugees who had crossed over.

The border provinces of Latakia, Idlib and Aleppo have seen a sharp upsurge of activity by the rebel Free Syrian Army in recent weeks, exacting a growing toll on loyalists of the Assad regime.

Rebels killed 26 government supporters -- most of them loyalist militiamen -- in the Daret Azzeh area of Aleppo province not far from the Turkish border on Friday, the Syrian Observatory for Human Rights said.

They were among 116 people killed in violence during the day. Seven children were among 69 civilians killed. Shelling by government forces of rebel neighbourhoods of the eastern city of Deir Ezzor killed 34 of the civilians, the Britain-based watchdog said.