Syrian Deputy Foreign Minister Faisal Mekdad has referred to Israel's attack on a military research facility a "declaration of war".
In an interview with CNN, he says the attack represents an alliance between terrorists and Israel, and that Syria would retaliate in its own time and way.
Israel is yet to confirm the strike, but sources say it targeted weapons bound for Hezbollah militants in Lebanon.
Syria has condemned the Israeli airstrikes against targets around Damascus, saying the attacks aim “to give direct military support to terrorist groups” fighting the government.
The Syrian Foreign Ministry also said today in a letter sent to the United Nations and the UN Security Council that the “Israeli aggression” killed and wounded several people and “caused widespread destruction”.
Syria’s government refers to rebels trying to topple president Bashar Assad’s regime as “terrorists”.
Israeli warplanes struck areas in and around the Syrian capital, setting off a series of explosions as they targeted a shipment of Iranian-made guided missiles believed to be bound for Lebanon’s Hezbollah militant group.
The attack, the second in three days and the third this year, signalled a sharp escalation of Israel’s involvement in Syria’s bloody civil war.
Syrian state media reported that Israeli missiles struck a military and scientific research centre near Damascus and caused casualties.
While the government tried to use the attacks to taint the rebels by linking them to Israel, Syria’s arch rival, the airstrikes still pose a dilemma for an Assad regime already battling a relentless rebellion at home.
If it fails to respond, it looks weak and opens the door to such airstrikes becoming a common occurrence. But any military retaliation against Israel would risk dragging the Jewish state and its powerful army into a broader conflict.
The tempo of the new strikes added a dangerous dynamic to the conflict, fuelling concerns that events could spin out of control and spark regional crisis.
Israel’s military today deployed two batteries of its Iron Dome rocket defence system to the north of the country. It described the move as part of “ongoing situational assessments”.
A senior Israeli official, who spoke on condition of anonymity in order to disclose information about a secret military operation to the media, confirmed that Israel launched an airstrike in the Syrian capital but did not give more precise details about the location.
The target was Fateh-110 missiles, which have precision guidance systems with better aim than anything Hezbollah is known to have in its arsenal, the official told The Associated Press.
The airstrikes come as Washington considers how to respond to indications that the Syrian regime may have used chemical weapons in its civil war.
President Barack Obama has described the use of such weapons as a “red line” and the administration is weighing its options – including possible military action.
Iran, a close ally of the Assad regime, condemned the airstrikes but gave no other hints of a possible stronger response from Tehran.
Israel has said it wants to stay out of the Syrian war, but prime minister Benjamin Netanyahu has repeatedly stated the Jewish state would be prepared to take military action to prevent sophisticated weapons from flowing from Syria to Hezbollah or other extremist groups.
Israel and Hezbollah fought a month-long war in mid-2006 that ended in a stalemate. The militant group is believed to have restocked its arsenal since that conflict with tens of thousands of rockets and missiles.
Earlier this year, the Iron Dome system was credited with shooting down hundreds of rockets during a round of fighting against Hamas militants in the Gaza Strip.
Israel is especially concerned that Hezbollah will take advantage of the chaos in neighbouring Syria and try to smuggle advanced weapons into Lebanon. These include anti-aircraft missiles, which could hamper Israel’s ability to operate in Lebanese skies, and advanced Yakhont missiles that are used to attack naval ships from the coast.
Syria’s state news agency reported explosions at the Jamraya military and scientific research centre near Damascus and said initial reports indicate they were the “result of Israeli missiles.” It said there were casualties but did not give a number.
Damascus-based activist Maath al-Shami said the strikes occurred around 3am. “Damascus shook. The explosion was very, very strong,” said Mr al-Shami, adding that one of the attacks occurred near the capital’s Qasioun mountain that overlooks Damascus.
He said the raid targeted a military position for the elite Republican Guards that is in charge of protecting Damascus, Assad’s seat of power.
Mohammed Saeed, another activist who lives in the Damascus suburb of Douma, said “the explosions were so strong that earth shook under us.” He said the smell of the fire caused by the air raid near Qasioun was noticeable miles away.