The Israeli leader has met with Putin numerous times since Russia's military intervention in Syria began three years ago.
"The IDF will continue to operate determinedly and decisively against any attempts to hurt Israeli civilians and breaches of Israeli sovereignty".
Israel will not dismiss the possibility of future relations with Syrian President Bashar al-Assad, Defence Minister Avigdor Lieberman said on Tuesday.
Israeli air strikes on Wednesday hit Syrian army positions in the southwest of the country near the occupied Golan Heights, state news agency SANA said.
The Netanyahu government is detemined to keep fighters loyal to Assad and to Iran out of the Syrian Golan border area near Israel. It bombed Iranian targets in Syria in response to that incident.
Russian Defense Minister Sergei Shoigu said Moscow is ready to discuss the issue of supplying Syria with the S-300 missile system.
Iran is backing Syrian President Bashar al-Assad in the war, as is Russian Federation.
Israel is particularly anxious about the presence of Damascus ally Iran next door in Syria.
"Using a Patriot battery, the IDF intercepted an unmanned aerial vehicle that infiltrated from Syria into Israeli territory", the IDF said in a statement.
Watched by Israeli soldiers with night-vision equipment, one woman - carrying one child and holding the hand of another - stepped through a gate built into Israel's security fence in the occupied Golan Heights.
He said the incursion threatened "the safety and security of Israel's northern cities and towns" and added that Israel has "repeatedly warned the Security Council of the destabilizing activities taking place in Syria and the threats they pose to Israel and the Middle East".