The Syrian army accused Israel of launching a dawn strike targeting a military research centre in Jamraya, near Damascus, in a statement carried by state news agency SANA.
"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 general command said.
The warplanes entered Syria's airspace via Mount Hermon, or Jabal el-Sheikh in Arabic, at low altitude and under the radar, the army said, adding that two site workers were killed.
"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 also denied reports Israeli forces had launched a 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.
The United States declined to comment on the reported strike by Israel, whose military intelligence chief Aviv Kochavi is currently in Washington for talks with top US general Martin Dempsey.
"I'd refer you to the government of Israel for questions about deliberations or actions that they may or may not have taken," White House spokesman Jay Carney said.
The reported air strike came after the UN and Arab League envoy to Syria, Lakhdar Brahimi, issued a fresh warning of the conflict spilling over.
"None of the neighbours is immune to the fallout consequences of the conflict," he told the UN Security Council.
International efforts have so far failed to end the conflict, which flared when regime forces launched a bloody crackdown on Arab Spring-inspired protests that erupted in March 2011.
In a surprise move on Wednesday, opposition chief Moaz al-Khatib said on his Facebook page that he was ready for conditional talks with Assad's representatives.
The Syrian National Coalition leader said the conditions included releasing "160,000 detainees" and that embassies abroad renew the passports of exiled citizens.
Until now, Syria's main opposition groups have said they are prepared to talk only if Assad steps down.
"I announce I am ready for direct discussions with representatives of the Syrian regime in Cairo, Tunis or Istanbul," Khatib said.
"While it is not right for anyone to bargain with the freedom for which our people have paid so dearly in blood, I say there are basic conditions before I sit down with representatives of the regime."
But he added that "we cannot trust a regime that kills children, attacks bakeries bombards universities, destroys Syria's infrastructure and massacres innocent people."
Assad proposed earlier this month a national dialogue, but made it clear this would apply only to groups not linked to the armed insurgency, effectively excluding the National Coalition.
Khatib said the unprecedented statement expressed his own opinion only and that his group would meet on Thursday to discuss the proposal.
Influential opposition group the Syrian National Council -- a key component of the Coalition -- swiftly rejected his proposal.
"The Syrian people have -- and are still paying -- an extremely high price for their full freedom and to get rid of every last remnant of this oppressive, tyrannical regime," said the SNC, adding that it "rejects any settlement or negotiation with the Syrian regime."
The coalition lashed out at the "global inaction" it said was giving Assad's regime a licence to kill, blaming his forces for the deaths of at least 78 people whose bodies were found on Tuesday in a river in the northern city of Aleppo.
Violence nationwide on Wednesday killed another 102 people, said the Syrian Observatory for Human Rights, adding to a grim overall death toll that the UN says tops 60,000.