"We agreed to continue contacts - both on the personal level and between our organizations, special services," Putin said.
The talks also involved Russian Foreign Intelligence Service chief Mikhail Fradkov and defence ministry representatives.
The Russian president said he and Netanyahu agreed that continuation of the armed conflict in Syria is fraught with pernicious consequences both for that country and the entire region.
Putin urged all the parties concerned to try not to aggravate the situation in Syria.
"A negative scenario may only be prevented by the earliest termination of the armed conflict and transition to a political settlement," Putin said.
"It is particularly important to avoid any actions that may sway the situation," he added.
It was not immediately clear whether the two leaders discussed arms deliveries to Damascus.
A high-ranking source in Jerusalem told RIA Novosti that Netanyahu would discuss Russian weapons supplies to Syria. Israel's Haaretz daily said Netanyahu was likely to ask Putin not to supply advanced S-300 air defence missile systems to Syria.
About 70,000 people have died in Syria since the beginning of the uprising against President Bashar Assad, according to UN figures.