Sergei Shoigu said at the start of the meeting with Turkish counterpart Hulusi Akar that they need to solve a few remaining issues ahead of Thursday's meeting of the presidents of Russia, Turkey and Iran in Sochi.
Russia, Turkey Defence Ministers Akar hailed the talks as a significant contribution to peace and stability in the region.
Russia and Turkey share a strong opposition to the US military presence in Syria and are coordinating ahead of the planned withdrawal of American troops.
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Iran and Russia are close allies of Syrian President Bashar Assad, while Turkey supports the opposition.
The three have arranged local truces in different parts of the war-torn country in recent years.