Tokyo's Construction and Transport Ministry, along with the city's rail operators, is planning to build new sidings along shared routes to cut delays.
The plan also includes improving infrastructure for information sharing between rail companies as well to provide better travel information to passengers.
The rail service in and around Japan's capital city has been suffering frequent delays in recent years due to a rise in the number of rail lines shared by rail companies such as East Japan Railway, Tokyo Metro and other private railway firms.
The length of shared tracks in the city and its suburbs totalled 922km in 2008, a 72% rise since 1990.
The ministry has called for investment by the rail firms to finance research and subsidies to improve station facilities.