Accountability in Government Act of 2006 - Prohibits a federal agency head from continuing in office without reappointment by the President, with the advice and consent of the Senate, in any case in which the Comptroller General's annual report under the Federal Financial Management Improvement Act of 1996 states that the agency is not in substantial compliance with federal financial management systems requirements, applicable accounting standards, and the U.S. Government Standard Ledger at the transaction level.