Israeli military spokesman Lt. Col. Jonathan Conricus said the drone was constantly monitored and that it traveled about 10 kilometers (6.2 miles) inside Israeli territory. "Obviously, our focus is on Syria and Iran".
Mr Putin and Mr Netanyahu had reportedly reached an agreement for Russian Federation to hold back Iranian-backed groups from the border before the Syrian regime began its offensive against rebels there last month.
However, there have recently been signs of an emerging compromise among key players.
"They (Russia) have an active interest in seeing a stable Assad regime and we in getting the Iranians out".
The attack late Wednesday night was near Hader at the frontier of the Israeli-occupied Golan Heights and caused only material damages, Syrian state news agency SANA cited a military source as saying. Russian Federation also has maintained warm ties with Israel and demonstrated a readiness to take its security interests into account.
"We won't take action against the Assad regime", the official quoted Mr Netanyahu as telling Mr Putin in Moscow.
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Meanwhile, Ali Akbar Velayati, a senior adviser to Iran's Supreme Leader Ayatollah Ali Khamenei, also left for Moscow on Wednesday for a meeting with Putin.
Israel fired a Patriot missile at an unmanned drone that entered its airspace from Syria on Wednesday, the military said, warning it would not tolerate such infiltrations, which have occurred several times over the past year.
"The IDF will not allow any violation of Israeli airspace and will act against any attempt to hurt its civilians", the IDF added.
The Israeli Defence Force tweeted early on Thursday morning to confirm they had targeted "three military posts" in Syria earlier that evening. Israel captured much of the strategic plateau in the 1967 war with Syria and annexed it in a move not recognised internationally.
Israeli cabinet ministers threatened this week to fire on Syrian forces that enter the Golan buffer zone set up as part of a 1974 United Nations -monitored armistice. "In that context, we rely on peaceful diplomatic means to resolve any differences and expect both sides to show restraint".