The tallest building in Japan presently is not in Tokyo, but in Osaka. Abenobashi Terminal Building Skyscraper (Abeno Harukas) at 300 meters nearly matches the Tokyo Tower at 333 meters.

The Mitsubishi Jisho construction company is all set to best that record by a whole 90 meters at 390 meters and build a skyscraper near the Tokyo Station by 2027!!!! Although this will not be completed by the Olympics, but still by 2027, lot of changes coming to the metropolis post Olympics too!.The awesome skyscraper will come up on the left side of the Tokyo Station if you see from the Marunouchi side of the station (or North exit of the Yaesu Exit). This building surpases Landmark Tower at 296 meters and Toranomon Hills at 255 meters. The 250 meters height tower building will begin operations in 2023 itself although the construction to reach 390 will continue in parallel. The commercial offices which will be housed in this building will be worth watching. The skyscraper although will be the tallest in Japan, will still be around position 20th worldwide. Those Dubai structures are just unbeatable. The Tokyo Station area is presently undergoing change and will continue to do so in the next decade too. Look forward to this addition although the completion is nearly 12 years away.
I had taken the below snap of the Tokyo Tower from JP Tower (Kitte Marunouchi) which I believe will be the spot from where you can contrast the Tokyo Station and this new skyscraper in the background.