"We will continue to act decisively against any spillover and any infiltration of Israeli territory or airspace", Netanyahu said. "We expect everyone to respect our sovereignty and for Syria to carefully abide by the ceasefire agreements".
He added that military officials believe the drone was Syrian and that it could have been on an intelligence collecting mission, but it was not yet clear if it purposely entered Israel or strayed from its path. "I am not sure that they are counting on the right man. Israel's real card in Syria may be Assad".
The shoot-down came weeks after Israeli forces fired at another drone from Syria.
"At the moment, Assad needs Russian fighter jets and militias that are commanded by Iran, but afterwards, when he controls the whole of Syria and emerges as the major victor in the civil war, he will want to go back to being the only ruler".
"Using a Patriot battery, the IDF intercepted an unmanned aerial vehicle that infiltrated from Syria into Israeli territory", the IDF said in a statement.
Netanyahu thinks it is now possible to hunt several birds: the Iranian presence, Lebanon, Golan and ending the state of war through the real deal of the century.
Israel has repeatedly said it will not allow Iran, or its Shiite proxies, to establish a permanent presence in postwar Syria.
In the ensuing years, Israel has rarely commented on targeted strikes against Iranian convoys attempting to deliver weapons to Hezbollah in Lebanon or airstrikes against Iranian military bases in Syria. An Israeli warplane was shot down during the reprisal.
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Russia, another key ally of Assad, has warned it's unrealistic to expect Iran to fully withdraw from the country but there have been signs of an emerging compromise.
Ali Akbar Velayati, a senior adviser to Iran's Supreme Leader Ayatollah Ali Khamenei, was also traveling Wednesday to Moscow for a meeting with Putin.
In their Moscow meeting Netanyahu and Putin were to discuss Syria.
While Russia and Iran have both deployed forces to Syria to help prop up Assad's government, their interests don't always converge.
Netanyahu underlined warm ties between Russian Federation and Israel, emphasizing what he described as their key stabilizing role for the Mideast. On July 6, Israel struck a Syrian post that it said had shelled the Golan buffer zone.
Russian Defense Minister Sergei Shoigu said in an interview with Italian newspaper Il Giornale published Wednesday that Moscow hopes that Israel and Iran will both display caution and avoid a showdown.
Assad's Russian-backed forces have advanced in southwest Syria and are on course to reach Quneitra, a rebel-held district abutting the Golan Heights frontier with Israel.