Ferry Transportation Enhancement Act of 2003 - Amends the Intermodal Surface Transportation Efficiency Act of 1991 to authorize appropriations for FY 2004 through 2009 for construction of ferry boats and ferry terminal facilities.
Amends Federal highway law to make ferry maintenance (currently, only terminal) facilities eligible for Federal funding.
Amends Federal transportation law to include ferries within the Federal clean fuels program.
Directs the Secretary of Transportation to: (1) establish a Ferry Joint Program Office to coordinate Federal programs affecting ferry boat and facility construction, maintenance, and operation, and to promote ferry service as a component of the Nation's transportation system; (2) maintain a national ferry database containing ferry routes, vessels, passengers and vehicles carried, funding sources, and related information; and (3) make grants to an institution of higher education to establish a National Ferry Transportation Institute for research, development, training programs, etc. relating to U.S. ferry transportation systems.