A general, two colonels, two majors and about 30 other soldiers are said to have crossed into Hatay province on Sunday night.
They were part of a group of some 200 people who crossed the border overnight into Monday, Anatolia news agency says.
Tensions between the two countries have escalated over the shooting down by Syria of a Turkish F-4 jet on Friday.
The two pilots were reported missing after their plane went down in the Mediterranean off the Syrian coast.
Syria has insisted the plane was engaged while in its airspace while Turkey insists it was in international airspace, 13 nautical miles from Syria, when it went down.
In a news conference broadcast by Syrian state TV on Monday, Foreign Ministry spokesman Jihad Makdissi said wreckage from the plane proved it had been shot down within Syrian waters.
“The Syrian defense forces used an anti-aircraft gun with the longest range of 1.2km. We can confirm the damage was caused by anti-aircraft fire. We didn’t use radar for this action.”
Syria was committed to good neighborly relations with Turkey, Jihad Makdissi said, adding that if Turkey responded positively, Syria would act accordingly.
The EU, which has urged Turkey to adopt a “restrained response”, is to extend its sanctions on Damascus in order to increase pressure on Bashar al-Assad’s government.
As the search in the Mediterranean continues for the F-4’s two pilots, Turkish media report that their boots have been found, but not their parachutes.
The Turkish cabinet discussed the crisis on Monday, a day before NATO ambassadors in Brussels were due to consider their response.
Ankara has invoked Article 4 of NATO’s charter, under which consultations can be requested when an ally feels its security is threatened.
More than 33,000 people have fled into Turkey since Syria’s violence began in March 2011.
The latest arrivals came over the border crossing near the town of Reyhanli.
They came with their families and were taken to Apaydin camp a few miles inside the border, Anatolia reports.
This is one of the biggest single groups of soldiers to defect to Turkey.
There has been a steady trickle of defections from the Syrian armed forces over the past year, most of them to opposition forces fighting inside the country.
So far there is no evidence that they have had a significant impact on the Syrian military’s ability to fight.
Turkey has openly supported the opposition Free Syrian Army which is largely made up of defectors.
The Turkish authorities say that 12 Syrian generals have already defected. Last week a Syrian air force pilot was granted political asylum after flying his plane to Jordan.
A senior UN human rights investigator is reported to have been allowed into Syria for the first time since the UN Human Rights Council set up a commission of inquiry into the escalation of violence.
Paulo Pinheiro is due to present his commission’s latest findings in Geneva on Wednesday. He is seeking to convince senior officials in Damascus to allow an investigation into a number of atrocities that have taken place.
The head of the UN observer mission has also had talks with Syrian government figures, nine days after his 300-strong team suspended its patrols in Syria because of the scale of the violence.
“We had a very professional exchange on that and we’ll see in the coming days what will happen next,” Maj. Gen. Robert Mood said.
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