Putin made a stopover at the Hemeimeem air base in Syria's coastal province of Latakia while en route to Egypt.
The base, in the heartland of Syrian President Bashar Assad's Alawite minority, has served as the main foothold for the Russian military campaign in Syria.
Speaking to the Russian troops at the base, Putin said that he had ordered the military to withdraw a "significant part" of the Russian contingent in Syria.
He added in remarks carried by Russian news agencies that "if the terrorists again raise their heads, we will deal such blows to them they have never seen."
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The Russian military has said previously that they will maintain their presence at the Hemeimeem air base and the naval facility in Tartus.
The visit marks Putin's first trip to Syria and comes as Assad's forces have retaken control over most of Syria under the Russian air cover.
Russia launched its air campaign in Syria on September 30 2015 when Assad's government was teetering on the brink of collapse and helped change the course of the conflict in its favor.