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"Around 01:40am, Israeli military aircraft over the occupied territories and south Lebanon launched an aerial aggression by firing missiles against three positions belonging to the armed forces of the Syrian Arab Republic," the letter said.
Syria uses the term "occupied territories" to refer to Israel and the occupied West Bank, Gaza Strip and Golan Heights.
A diplomatic source in Beirut told AFP the three sites were the Jamraya military facility, a nearby weapons depot and an anti-aircraft unit in Sabura, west of the capital.
"This aggression caused deaths and injuries and serious destruction at the sites and in the surrounding civilian regions," the letter added.
The cabinet held an emergency meeting, warning afterwards that "the aggression opens the door wide to all possibilities."
"The international community should know that the complex situation in the region has become more dangerous after this aggression."
The foreign ministry letter said the strikes were evidence that Israel was working with "terrorist groups" including the rebel jihadist Al-Nusra Front, which has pledged allegiance to Al-Qaeda.
"The blatant Israeli aggression against military sites in Syria confirms the coordination between Israel and terrorist groups," it said.
"This leaves no doubt that Israel is the beneficiary, the engine and sometimes the executor of the terrorist attacks taking place in Syria against the state and the people."
UN Secretary General Ban Ki-moon expressed "grave concern", his spokesman Martin Nesirky said.
"The secretary general calls on all sides to exercise maximum calm and restraint, and to act with a sense of responsibility to prevent an escalation of what is already a devastating and highly dangerous conflict," Nesirky said.
Syrian state television Al-Ikhbariyah later quoted unnamed sources as saying its forces were ready to retaliate if new "violations" occur.
"The Syrian missiles are ready to strike specific targets in case of any (further) violations," it said quoting the unidentified sources.
Egypt condemned the strikes as a "violation" of international law and the Cairo-based Arab League demanded UN Security Council intervention to stop such Israeli attacks.
Iran's Defence Minister General Ahmad Vahidi said "the assault, which was carried out with the US green light, unveils the links between the terrorist mercenaries and their masters of the Zionist regime."
Britain warned of the "increasing danger to the peace of that entire region from the Syria crisis just getting worse and worse."
Turkish Prime Minister Recep Tayyip Erdogan, meanwhile, delivered his harshest attack yet against President Bashar al-Assad, calling him a "butcher" and warning he will "receive his judgment in this world" for the deaths of thousands of Syrians.
More than 70,000 people have been killed in Syria in just over two years.
Sunday's strike came around 48 hours after a reported Israeli raid on a weapons storage facility at Damascus airport.
Residents of the upscale Damascus neighbourhood of Dumar said Sunday's strike turned night into day.
"It was like an earthquake, the sky was yellow and red," said 72-year-old Najwa.
Video footage on YouTube appeared to show missiles lighting up clouds, blazing fires, and an explosion producing a massive orange fireball.
Israel reportedly targeted the Jamraya facility earlier this year, in a January 30 raid that Israeli officials have implicitly acknowledged.
The Jewish state has frequently warned it would act to stop the transfer of advanced weapons systems or chemical weapons to Lebanon's Hezbollah, with which it fought a devastating war in 2006.
Hezbollah and Iran, Israel's regional arch-foes, have steadfastly backed the Assad regime since the uprising erupted in March 2011.
US President Barack Obama, speaking after the first reported attack this week, said Israel was justified in protecting itself.
"The Israelis justifiably have to guard against the transfer of advanced weaponry to terrorist organisations like Hezbollah," he said, without commenting directly on the strike.
"We coordinate closely with the Israelis, recognising that they are very close to Syria, they are very close to Lebanon."
The rebel Free Syrian Army reacted cautiously, saying the country was already under daily attack by regime aircraft, while the opposition National Coalition said Israel had "taken advantage" of the conflict.
Israel boosted security measures, deploying two batteries of the Iron Dome missile defence system to the north and closing airspace there until May 9, the military said.
A senior Israeli source said the air force was on "high alert" and media reports said security was boosted at Israeli embassies worldwide.
The strikes came after the Syrian Observatory for Human Rights reported that the bodies of at least 62 people had been found on Saturday in a Sunni district of the port of Banias after a regime assault, and warned of fresh "massacres".
At least 35 people were killed in violence on Sunday, the Observatory said, adding that rebels also seized part of the Minnigh military airport where a regime general was killed on Saturday.
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Syria uses the term "occupied territories" to refer to Israel and the occupied West Bank, Gaza Strip and Golan Heights.
A diplomatic source in Beirut told AFP the three sites were the Jamraya military facility, a nearby weapons depot and an anti-aircraft unit in Sabura, west of the capital.
"This aggression caused deaths and injuries and serious destruction at the sites and in the surrounding civilian regions," the letter added.
The cabinet held an emergency meeting, warning afterwards that "the aggression opens the door wide to all possibilities."
"The international community should know that the complex situation in the region has become more dangerous after this aggression."
The foreign ministry letter said the strikes were evidence that Israel was working with "terrorist groups" including the rebel jihadist Al-Nusra Front, which has pledged allegiance to Al-Qaeda.
"The blatant Israeli aggression against military sites in Syria confirms the coordination between Israel and terrorist groups," it said.
"This leaves no doubt that Israel is the beneficiary, the engine and sometimes the executor of the terrorist attacks taking place in Syria against the state and the people."
UN Secretary General Ban Ki-moon expressed "grave concern", his spokesman Martin Nesirky said.
"The secretary general calls on all sides to exercise maximum calm and restraint, and to act with a sense of responsibility to prevent an escalation of what is already a devastating and highly dangerous conflict," Nesirky said.
Syrian state television Al-Ikhbariyah later quoted unnamed sources as saying its forces were ready to retaliate if new "violations" occur.
"The Syrian missiles are ready to strike specific targets in case of any (further) violations," it said quoting the unidentified sources.
Egypt condemned the strikes as a "violation" of international law and the Cairo-based Arab League demanded UN Security Council intervention to stop such Israeli attacks.
Iran's Defence Minister General Ahmad Vahidi said "the assault, which was carried out with the US green light, unveils the links between the terrorist mercenaries and their masters of the Zionist regime."
Britain warned of the "increasing danger to the peace of that entire region from the Syria crisis just getting worse and worse."
Turkish Prime Minister Recep Tayyip Erdogan, meanwhile, delivered his harshest attack yet against President Bashar al-Assad, calling him a "butcher" and warning he will "receive his judgment in this world" for the deaths of thousands of Syrians.
More than 70,000 people have been killed in Syria in just over two years.
Sunday's strike came around 48 hours after a reported Israeli raid on a weapons storage facility at Damascus airport.
Residents of the upscale Damascus neighbourhood of Dumar said Sunday's strike turned night into day.
"It was like an earthquake, the sky was yellow and red," said 72-year-old Najwa.
Video footage on YouTube appeared to show missiles lighting up clouds, blazing fires, and an explosion producing a massive orange fireball.
Israel reportedly targeted the Jamraya facility earlier this year, in a January 30 raid that Israeli officials have implicitly acknowledged.
The Jewish state has frequently warned it would act to stop the transfer of advanced weapons systems or chemical weapons to Lebanon's Hezbollah, with which it fought a devastating war in 2006.
Hezbollah and Iran, Israel's regional arch-foes, have steadfastly backed the Assad regime since the uprising erupted in March 2011.
US President Barack Obama, speaking after the first reported attack this week, said Israel was justified in protecting itself.
"The Israelis justifiably have to guard against the transfer of advanced weaponry to terrorist organisations like Hezbollah," he said, without commenting directly on the strike.
"We coordinate closely with the Israelis, recognising that they are very close to Syria, they are very close to Lebanon."
The rebel Free Syrian Army reacted cautiously, saying the country was already under daily attack by regime aircraft, while the opposition National Coalition said Israel had "taken advantage" of the conflict.
Israel boosted security measures, deploying two batteries of the Iron Dome missile defence system to the north and closing airspace there until May 9, the military said.
A senior Israeli source said the air force was on "high alert" and media reports said security was boosted at Israeli embassies worldwide.
The strikes came after the Syrian Observatory for Human Rights reported that the bodies of at least 62 people had been found on Saturday in a Sunni district of the port of Banias after a regime assault, and warned of fresh "massacres".
At least 35 people were killed in violence on Sunday, the Observatory said, adding that rebels also seized part of the Minnigh military airport where a regime general was killed on Saturday.
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