Sony announced today that a new, large stock of PlayStation VR going to arrives in Japan on December 17, 2016.
After October 13, 2016 when the device released the PlayStation VR available rarely in the country and from December 17 you can buy it not just from the Sony stores but from other official retailers like the GEO, TSUTAYA, Yamada Denki and others.

The exactly store list where the PS VR will be available again from December 17 can be found in here: http://www.jp.playstation.com/psvr/shop/index.html