The Syrian army said that an Israeli air strike at dawn on Wednesday targeted a military research centre in Jamraya, near Damascus.
"Israeli fighter jets violated our airspace at dawn today and carried out a direct strike on a scientific research centre in charge of raising our level of resistance and self-defence," the army's general command said in a statement carried by state news agency SANA.
The strike came "after terrorist groups made several failed attempts in the past months to take control of the site," the statement added of rebel groups fighting the regime of President Bashar al-Assad.
Israeli warplanes entered Syrian airspace via Mount Hermon, or Jabal el-Sheikh in Arabic, at low altitude and under the radar, the army said.
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"They... carried out an act of aggression, bombarding the site, causing large-scale material damage and destroying the building," state television quoted the military as saying.
The army added that two site workers were killed in the strike.
"This assault is one of a long list of acts of aggression and criminality against the Arabs and Muslims," said the statement.
The army denied earlier reports that Israeli forces had launched an air strike overnight on a weapons convoy from Syria near the border with Lebanon.
Israel has expressed concern that Syria's stockpile of chemical weapons could fall into the hands of Lebanon's Shiite Hezbollah group, an ally of the Damascus regime, or other militant organisations.