Alternative Energy Refueling System Act of 2006 - Amends the Solid Waste Disposal Act to require the Administrator of the Environmental Protection Agency (EPA) to establish a program to provide eligible entities (refueling vendors or owners or operators of a facility where an alternative energy refueling system is located), for FY2007-FY2011, reimbursement from the Leaking Underground Storage Tank Trust Fund for a portion of the costs of purchasing and installing one or more alternative energy refueling systems (systems used to refuel motor vehicles with an alternative fuel such as compressed natural gas or E-85 ethanol).
Prohibits an entity that receives a federal tax credit for placing in service a qualified alternative fuel vehicle refueling property from receiving reimbursement under this Act if the system cost was taken into consideration in calculating the tax credit. Limits reimbursement to: (1) two systems for each facility owned by an eligible entity; and (2) the lesser of 30% of a system's cost or $30,000.