Netanyahu was accompanied by his army and intelligence chiefs in a rare step for an overseas visit that Israel said would focus on Russia's manoeuvring in the war-torn nation.
"It was very important to come here in order to clarify our position and to do everything to avoid any misunderstandings between our forces," Netanyahu said at the start of the meeting.
Netanyahu said he was determined to stop arms deliveries to Lebanon's Shiite Hezbollah movement and accused Syria's army and Iran of trying to create a "second front" against Israel.
"We know and understand that the Syrian army and Syria in general is in such a state that it isn't up to opening a second front - it is trying to maintain its own statehood," he said in comments broadcast on Russian television.
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The United States has said Russia - one of the few remaining allies of President Bashar al-Assad - recently sent troops, artillery and aircraft to Syria, sparking fears that Moscow could be preparing to fight alongside government forces.
Reports in the Israeli press said that the aim of Netanyahu's Moscow visit was to avoid any possible clashes between Israeli and Russian jets that could operate over Syria.
Israeli military officials reportedly fear that any Russian air presence could cut their room for manoeuvre after several purported strikes on Iranian arms transfers to Hezbollah through Syria in recent months that were not officially acknowledged by Israeli authorities.
Israel opposes Assad's regime but has sought to avoid being dragged into the conflict in neighbouring Syria.
It also fears that Iran could increase its support for Hezbollah and other militant groups as international sanctions are gradually lifted under a July nuclear deal that Moscow helped negotiate between Tehran and world powers.