Israeli Prime Minister Benjamin Netanyahu on Wednesday met Russian President Vladimir Putin, discussing security in the Middle East with a focus on Iran.

During the talks at the Kremlin, the two leaders were also set to discuss how to coordinate and avoid military clashes on Syrian territory, where Israel is taking action against Iran.

"The biggest threat to stability and security of the region is Iran, and we will do everything to prevent this threat," Netanyahu said in opening remarks translated into Russian before closed-door negotiations.

Iran, Hezbollah and Russia are allies of Syrian President Bashar al-Assad. Netanyahu has stressed that he will not let Israel's arch-foe Iran use Syrian territory as a base for its military.

Prior to his Moscow visit, Netanyahu said the talks will focus on "preventing Iran from entrenching in Syria, the entrenchment of a country which explicitly says that its goal is to wipe us out."

He is accompanied in Moscow by his national security advisor Meir Ben-Shabbat and head of military intelligence Tamir Heiman.

On Sunday, the Israeli prime minister said talks with Putin will be "very important" to ensure Israel's freedom to act against Iran and Hezbollah in Syria while avoiding frictions with Russian forces.

Wednesday's talks, which Israel postponed by several days, is the first extended face-to-face meeting since September 17, when Syria's air defence systems took down a Russian plane by mistake during an Israeli airforce operation.

The resultant deaths of 15 Russian troops caused serious tensions between Israel and Russia. Netanyahu and Putin have spoken several times since the incident, and had a brief encounter in Paris in November.

Netanyahu said his primary goal in Moscow was "to ensure that the Russian military and the IDF (Israel Defense Force) coordinate in such a manner so as to prevent friction and clashes between us," he said Wednesday.