This research aims to give an overview of Japans national-level transport planning schemes, and to discuss interplays between them and recoveries from natural disasters. In the first part, Japans national spatial development plans and long-term planning schemes for railway, road, port and airport infrastructures are reviewed and compared. In the second part, imbalance embedded in the current planning scheme for different modes are demonstrated making use of recent post-disaster reconstruction processes. A literature-based desktop research is carried out focusing on Japanese literature. These include, but not limited to, official government reports and planning documents, statistical data, and handbooks for experts in the field. All of the long-distance modes have their planning schemes with different levels of comprehensiveness and robustness for each mode. Expressways and high-speed railways have the most comprehensive and robust network plans, while conventional railway, airports and seaports have ones with limited extent. Because of this, post-disaster reconstruction processes from damages to the infrastructure work differently in particular for conventional railways and for expressways in rural areas, which are competitors against each other. Strong framework for intermodal and multimodal transport is still in lack in Japan. Important structural imbalance between modes, in particular between conventional railway and expressway exist, and it becomes obvious in case of a natural disaster. Multimodal planning, frameworks for flexible adjustment of once-made long-term plans, and addressing imbalances regarding robustness between railways and expressways are identified as future challenges of the countrys planning schemes.