Jacky Rowland, Al Jazeera's correspondent in Jerusalem, said: "All that Israel has said is that it did not carry out a military attack against Syria."
She said: "This has been a summer of heightening tensions between Israel and Syria, certainly in terms of rhetoric and talk ... this flurry of allegations and denials won't have helped."
A Syrian army spokesman told the official Sana news agency: "Enemy Israeli planes penetrated Syrian air space from the Mediterranean Sea heading towards the northeast, breaking the sound barrier."
He said: "Our air defences forced them to leave ... without causing human or material loss."
"What are they going to do with about $30m of armaments except attack neighbouring countries?"
Syrian government minister
"We warn the Israeli enemy government against this flagrant aggressive act, and retain the right to respond in an appropriate way," he said.
"Air defence units confronted them and forced them to leave after they dropped some ammunition in deserted areas without causing any human or material damage."
But asked by Al Jazeera if the Israeli jets had attacked targets in Syria, Buthayaa Shaaban, a Syrian government minister, would only confirm that the Israelis "intervened in our airspace".
She said: "The Israeli aeroplanes went into our airspace at night on our northern borders and this is not really surprising. What are they going to do with about $30m of armaments except attack neighbouring countries?"
She said that Syria was still looking into the "ammunition" that the Israeli jets are alleged to have dropped.
At the beginning of last summer's war against Hezbollah in Lebanon, Israeli aircraft flew over the palace of Bashar al-Assad, the Syrian president, in what analysts called a warning to Damascus.
In June of the same year, Israeli jets also flew over al-Assad's summer home in the coastal city of Latakia, after Syrian-backed Palestinian fighters in Gaza captured a young Israeli soldier.
Syria and Israel remain technically at a state of war.
Peace talks broke down in 2000 over the fate of the Israeli-occupied Golan Heights.