The two leaders have met more than a dozen times in recent years and the countries' militaries have been working to avoid accidental clashes in Syria, where Israel says it has carried out hundreds of strikes against Iranian targets to stop Tehran establishing a permanent military presence there.
"Security coordination between us is always important, but it is especially important now, since in the past month there has been a serious increase in attempts by Iran to hit Israel from Syria and to place there precision missiles to use against us," Netanyahu said at the start of the meeting.
Iran and Iran-backed Lebanese militia Hezbollah have helped President Bashar al-Assad in the Syrian civil war. Russia, which is also aiding Assad, has largely turned a blind eye to the Israeli air strikes.
Russia's RIA news said Putin praised military and security cooperation between Russia and Israel.
Following the talks, which lasted for several hours, Russian Foreign Minister Sergei Lavrov said both Russia and Israel agreed to boost dialog between their militaries in regards to Syria, Interfax news agency reported.
The news agency, also citing the minister, said that Putin and Netanyahu both underlined the need to safeguard Syria's territorial integrity and sovereignty.After an earlier meeting with Russian Defence Minister Sergei Shoigu, Netanyahu reiterated that for Israel to ensure its security, its military needed to have "freedom of action" against Iran in the region.