Federal Stimulus of Commercial Application of Energy Technology Act of 2006

Federal Stimulus of Commercial Application of Energy Technology Act of 2006 - Directs the Secretary of Energy to establish the Innovative Energy Technologies Fund for Federal Buildings (the Fund) and to administer the Fund to enable federal agencies to demonstrate innovative energy technologies for retrofit or new construction of federal buildings and facilities.

Allows federal agencies to apply to the Secretary for a loan for financing the demonstration of innovative energy technology projects and requires such agencies to repay the Fund from savings in energy, water, and other costs attributable to actions taken as a result of the project undertaken with the loan. Permits a federal agency, in addition to financing an innovative energy technology project, to use the loan amount to pay the costs of administration and proposal development and to acquire and operate equipment necessary to monitor and verify associated energy savings. Requires a federal agency to repay to the Fund the principal amount of the loan, plus interest at a rate determined by the Secretary.

Requires a federal agency to submit specified annual reports to the Secretary with respect to the installation of an innovative energy technology project for which a loan is provided under this Act in an amount greater than $1 million until the date that final repayment of the loan is due.

Requires the Secretary to transmit to Congress a report on the operations of the Fund and the total expenditures from the Fund to each federal agency.