Clean Energy Business Zone Act of 2009 and the Clean Energy Empowerment Zone Act of 2009 - Amends the Internal Revenue Code to: (1) authorize the Secretary of the Treasury to designate 40 clean energy business zones between 2009 and 2012; (2) allow an increased tax credit for wages paid in such a zone; (3) allow a work opportunity tax credit for wages paid to an employee in such a zone; (4) allow financing of any qualified Green building or clean energy facility with clean renewable energy bonds; (5) allow increased expensing of property in such a zone; and (6) allow an exclusion from gross income of gain from the sale or exchange or any clean energy business zone asset held for more than five years.
Amends the Small Business Act and the Small Business Investment Act of 1958 to waive loan fees for qualified Green building and clean energy facility loans made before 2020.