Yamaya (やまや), aka World Liquor System, is Japan’s largest bottle shop retail chain. Stores are dotted throughout the country from north to south and stock a variety of domestic and international brands, including a moderate range of whisky. Stores are not specifically dedicated to malt but the majority has a reasonably sized corner with an adequate range.
Perhaps one of the best things about Yamaya is the large stockpile and variety of domestic whisky at a very reasonable price. You can get anything from White Oak's Akashi single malt to a 25-year old expression from Yamazaki. With specialized wines as its core, the company prides itself on sourcing liquor and various accompanying food from all over the world. Yamaya boasts that it's recognized in Japan as a pioneer, both as an importer and a retailer. Perhaps that's something you can decide for your self by visiting one of the 254 (March 31,2020) stores.
For those who fancy an independent bottling and are looking for something special to reward your palate, there are some exceptional malts under lock and key available, with a price to go with it. As for standard bottlings of malt, a vast array can be found at any Yamaya store that will equally satisfy (presumably).
The store in the photos above is an effortless 2 stop train ride from JR Sannomiya (heading towards Osaka). Get off at the JR Rokkomichi station and head out the exit adjacent to the bus stop. Turn right and walk to the first set of traffic lights (100m), on the corner is a KFC. Here, turn right again and follow the road down another 500 meters and Yamaya is on the left hand side on the corner (at the main intersection).