The extensive underground network of train and metro lines in Tokyo looks like a roller coaster in tube if one looks at its 3D diagram. Even that, the deepest train station by means of relative to the surface is not in Tokyo. The deepest in operation station in Japan is the Doai Station 「土合駅」in Minakami, Gunma, Japan and operates by JR East company.
Doai Station. Image from http://sobatabi.exblog.jp/
This station is about 4 hours by train from Shinjuku, Tokyo via JR Shonan-Shinjuku Line and JR Joetsu Line including 2 transfers. There is a skiing park and ropeway nearby, other than that, there aren't much attractions there ( I will write a little about it), so you have been alerted, don't spend a total of 8 hours just to come here and find nothing except the deep platform.
Stairway to the surface. Image by Rsa, from Wikipedia
The station has 2 platforms, one is the underground platform at 70m below the surface. The other one is on the surface. The underground rail is for Northbound train to Nagaoka, while the surface platform is for Southbound train toward Minakami.
The number of steps from the underground platform to the surface is 486.
This underground platform is constructed in the Shin-Shimizu tunnel, when the tunnel opened on 27 September 1967. Originally Doai station was single track and was opened in 1936.
Doai Station is within the mountainous region, with Mount Tanigawa nearby. This mountain is listed in the top 100 famous mountain in Japan. Since 1930s, over 800 people had died there.
Since it is a mountainous region, winter will turn this place into a winter wonderland.
Winter at Doai Station. Image from wikipedia
- Tenjindaira ski area via Tanigawadake Ropeway
The ropeway is a bus ride away from Doai Station. If you decide to go to the ski area, please check the official website for weather and other information. The bus is operated by by Kanetsukotsu Bus and it stops in-front of the station. Both the ski area and the bus company websites are in Japanese.
My advice is that, it might better to take the bus from Minakami Station. The Minakami Station is a major station that provides train service to Ueno in Tokyo, therefore you could get clearer information there. There are also many buses from different travel companies from Tokyo during ski season too.