Russia is "actively carrying out construction of military compounds on the islands of Iturup and Kunashir", Shoigu said at a meeting with military top brass, according to the ministry`s website.
Relations between Moscow and Tokyo have been strained for decades because of the status of the four southernmost islands in the Kuril chain, known as the Northern Territories in Japan.
Some 19,000 Russians live on the remote rocky islands, occupied by Soviet troops in the dying days of World War II.
The two countries have never officially struck a peace treaty and the lingering tensions over the issue have hampered trade ties for decades.
The Russian ministry said the new military buildings would help "raise the combat readiness of troops on the eastern frontiers of Russia."
Altogether, Russia plans to put up 392 pre-fabricated buildings on the islands, including schools, kindergartens, leisure centres and dormitories, with construction work continuing through the winter.
"This year, the priority is finishing the most essential buildings and the engineering infrastructure" to receive troops and equipment, Shoigu said.
In September Russian Prime Minister Dmitry Medvedev visited the island of Iturup and surveyed troops there, angering Japan.
Russian Foreign Minister Sergei Lavrov has ruled out any compromise on the islands, telling his Japanese counterpart Fumio Kishida in September that Tokyo must acknowledge "the postwar historical realities."
Russia has recently poured in investments to the region and reconstructed the Japanese-built airport on Kunashir.
Russia building new military bases on islands claimed by Japan
02 December 2015
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Russia has begun building two modern military compounds on the far eastern Kuril islands, defence minister Sergei Shoigu said Tuesday, heightening long-running tensions with Japan over the disputed islands.
