"I order you to act as tough as possible," he told a defence meeting in televised remarks.
"Any targets threatening the Russian grouping or our land infrastructure should be immediately destroyed."
"I would like to warn those who would once again try to organise some sort of provocations against our servicemen," he said in a thinly veiled threat to Ankara.
Last month, Turkey shot down a Russian warplane on the Syrian border, claiming it violated Turkish airspace.
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Putin's call for a tougher military response is also likely to cause concern among monitors who have repeatedly accused Russia of conducting an indiscriminate bombing campaign and killing civilians in Syria.
Russia has been carrying out air strikes in the war-ravaged nation at the request of President Bashar al-Assad since the end of September, while a US-led coalition is conducting its own campaign targeting the Islamic State (IS) group.
Putin rejected claims that Russia is using the Syrian campaign, which also saw the military fire off cruise missiles from warships in the Caspean Sea, to showcase its top weapons to the West.
"Our actions there are not guided by some unclear abstract geopolitical interests, nor are they guided by a desire to practice and test new weapons systems which is of course important in itself," Putin said at the defence meeting.
Defence Minister Sergei Shoigu, for his part, said Islamic State jihadists now control 70 percent of Syrian territory, putting their number at 60,000.