"The most modern air defence systems S-400 were put on standby alert in the Leningrad region to protect military, administrative and civilian sites," the defence ministry said.
The S-400 surface-to-air missile is one of Russia's most advanced weapons.
A Saint Petersburg-based defence ministry official told AFP the systems replaced the previous S-300s but declined to say how many were placed there.
The missiles were first tested at a range in the southern region of Astrakhan before being transferred 2,000 kilometres (1,200 miles) to the north.
The S-400 system is also expected to be deployed this month in Russia's European exclave of Kaliningrad.
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