Data from 2003...may be outdated but here it is. I have no dog in this fight.
http://www.demographia.com/db-htld-rail.htm
Profitable Japanese Systems
There are two places in the world where rail’s success is not accompanied by excess costs and is felt throughout the urban area: Tokyo (Tokyo-Yokohama) and Osaka (Osaka-Kobe-Kyoto).
Violating the old transit myth that there are no profitable systems, data from the Union of International Public Transport (the international equivalent of the American Public Transportation Association) indicate both systems earn annual profits of approximately 30 percent over operating and capital expense.
In both urban areas, most service is provided by historic private suburban rail (commuter rail) companies that operate their own lines and share tracks with municipally owned subway systems. In addition, privatized units of Japanese National Railways (JNR) provide a large share of the travel. The municipally owned urban bus, rail, and monorail systems receive small subsidies, sometimes only for capital.
