Six Syrian soldiers were killed in Israeli drone strikes in the Damascus countryside, state-run El Ekhbariya TV reported early on Wednesday.
Syria and Israel are engaged in US-mediated talks on easing tensions in southern Syria, with Damascus seeking a security deal that could open the door to wider political negotiations.
Syria said on Monday that Israel had sent 60 soldiers into its territory near Mount Hermon in a violation of its sovereignty, while the Israeli military said its troops carried out a routine operation in southern Syria but not in Beit Jinn, an area close to the border with Lebanon and near Mount Hermon.
Syria's foreign ministry on Tuesday condemned the recent Israeli attacks on its territory, saying they pose a direct threat to regional peace and security.
It also condemned the Israeli forces' incursion into a town in the Quneitra countryside, their "arrest campaigns against civilians", and their "announcement of the continuation of their illegal presence on the summit of Mount Hermon and the buffer zone".
"These aggressive practices constitute a flagrant violation of the UN Charter, international law, and relevant Security Council resolutions, and constitute a direct threat to peace and security in the region".
The Israeli military said on Sunday that it had carried out "several activities last week in southern Syria to locate weapons and apprehend suspects".
Israel has repeatedly cited its own security concerns in its military interventions inside Syria since the fall of Bashar al-Assad last December, including what it sees as its obligation to protect members of the Druze minority in southern Syria.
It has carried out hundreds of strikes in Syria since Assad’s ouster. It has also opened talks with the interim authorities in Damascus.
Last week, Syrian Foreign Minister Asaad al-Shaibani met Israeli Strategic Affairs Minister Ron Dermer in Paris to push for a return to the arrangements that had been in place since a 1974 disengagement agreement.
In January, Israeli Defense Minister Israel Katz said Israeli troops would remain on the summit of Mount Hermon indefinitely.