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The embattled Syrian government denounced the grounding of the aircraft, calling the incident an example of "air piracy."
"They swam through the Orontes River," said a Turkish government official, who asked not to be identified because he was not authorized to discuss border security with the media. The Orontes makes up part of the border between Turkey and Syria.
Both countries have frozen diplomatic ties. This month, escalating tensions flared yet again, when Syrian artillery killed two women and three children in the Turkish border town of Akcakale. Since then, Turkey and Syria have repeatedly engaged in artillery duels along the 900-kilometer (560-mile) border dividing the two countries.
Unlike last week's unexpected grounding of a Syrian passenger plane flying from Moscow to Damascus, the inspection of the Armenian airplane appeared to have been agreed upon ahead of time by Armenian and Turkish authorities.
Turkey's prime minister has backed the Syrian opposition and provided a staging ground for rebels, while repeatedly calling on Syria's president to step down.
"They wanted to escape from the fighting," he said, adding that the 12 Syrian troops were being kept at a separate location from other camps housing refugees and defectors.
The Armenian cargo was eventually allowed to fly on to Syria after remaining grounded and searched in Turkey for at least five hours.
"We provided a license for use of our airspace provided they first make a 'technical landing.' "
Turkey's Foreign Ministry confirmed to CNN Turkish media reports that at least 12 Syrian soldiers, running away from clashes with Syrian rebels, escaped across the border and surrendered to Turkish border guards.
"An Armenian civilian cargo aircraft requested overflight permission from Yerevan to Aleppo," explained Selcuk Unal, a spokesman for Turkey's Foreign Ministry.
Istanbul (CNN) -- For the second time in a week, Turkish officials searched a civilian airplane headed to Syria in what appears to be the enforcement of a new Turkish air blockade against the Syrian government.
The Turkish government says it is a violation of international and Turkish law to transport military materials on civilian planes.
The English-language website for KBP Instrumental Design Bureau describes it as a "developer and manufacturer of high-precision weapons,Prada Handbag Online." Headquartered in Tula, Russia, the company advertises itself as a manufacturer of rocket systems, tanks, artillery, and short-range air defense systems.
After a search of the aircraft, Turkish authorities confiscated an unspecified number of items in the plane's cargo hold that officials said were being shipped to Syria's Ministry of Defense.
On Monday, Turkey's Foreign Ministry announced more than 100,000 refugees had now fled Syria to take shelter in Turkish refugee camps,http://www.pradahandbagoutletonline.com.
Armenian and Turkish diplomats confirmed to CNN that an Armenian cargo plane destined for the stopped first in the Turkish city of Erzurum for an inspection of its cargo Monday morning.
Unlike thousands of other soldiers and officers who have defected from the Syrian armed forces throughout the 19-month conflict,Prada Outlet, the Turkish official said the 12 new arrivals did not appear to be deserting the military.
"The plane is transporting humanitarian aid to Syria and its stop in Turkey was planned," Armenian Foreign Ministry spokesman Tigran Balayan wrote in an e-mail to CNN before the cargo was allowed to leave.
On Monday, Turkey's prime minister defended the decision to confiscate cargo from the Syrian plane.
"We are exercising our sovereign right," Unal added.
Also on Monday, the European Union added to Syria's growing isolation by announcing a 19th round of sanctions against the regime. One of the punitive measures bans Syrian Arab Airlines planes from all European Union airports.
Damascus has accused the Turkish government of arming and funding "terrorists."
Last Wednesday, Turkey made a conspicuous show of force, dispatching F-16 warplanes to escort the Syrian passenger plane headed from Moscow to Damascus to an unplanned stop in the Turkish capital, Ankara.
"This comes in addition to an existing ban on Syrian cargo flights," the EU Council announced in a news release.
"These containers that have been taken off the plane, the sender company is KBP Instrumental Design Bureau," Recep Tayyip Erdogan announced in a live television broadcast. "The receiver? The Syrian National Defence Ministry. This material that we confiscated is without a doubt military equipment,www.pradahandbagoutletonline.com. Calling it radar equipment or some other type of equipment is a deflection."
The once intimate relationship between the Turkish and Syrian governments is one of the many casualties of the Syrian civil war,Prada Handbag Outlet. Since Syrian security forces first began attacking anti-government protests in March 2011, Turkey and Syria have gone from lifting visa restrictions on each other's citizens and holding joint Cabinet meetings to routinely denouncing each other.
"Some of the soldiers are wounded and are being treated in hospital. They left their weapons in Syria," the Turkish official continued.
But over the weekend, a new kind of "refugee" fled to Turkey.
In the wake of the search and confiscation of the Syrian plane cargo, both Turkey and Syria have closed their airspace to each others' aircraft.