"The air defence regiment of the Russian Northern Fleet deployed on Yuzhny island of the Nova Zemlya archipelago has been completely reequipped with new S-400 systems," said a statement.
"The newest air defence systems increase the aerial zone in the region that falls under the control of our military," it added.
The S-400 were an upgrade of the S-300 systems and were developed in the 1990s.
The anti-aircraft weapon system has in recent years been deployed in Syria and has been purchased by NATO countries like Turkey, Efe news reported.
The official statement added that the missile system was already in operation in the Arctic in the Kola peninsula.
Last March, Russian Northern commander Nikolay Yevmenov said that Moscow would be upgrading its weapons in the Arctic to protect the Northern Sea Route, an alternative to the Suez Canal that had been made possible thanks to shrinking ice caps.
In recent years, Moscow has reinforced its military presence in the Arctic after President Vladimir Putin ordered the creation of a network of military bases in northern Russia and Siberia.
In the defence policy approved by Putin in 2014, the Arctic appears for the first time as a priority region for national interests.
During a visit two years ago to the Franz Josef Land, an archipelago inhabited exclusively by military personnel, Putin said that experts had advised that the Arctic continental shelf hosts almost a quarter of the planet's energy resources, while the Russian Arctic is home to 1.6 billion tonnes of hydrocarbons.
The US and Canada, among other countries, have criticized the Kremlin for deploying heavy weapons in places like Nova Zemlya, considered the largest nuclear dump on the planet by Greenpeace.
( With inputs from IANS )