September 11th Lessons Learned in Preventing Waste, Fraud, and Abuse Implementation Act of 2006

September 11th Lessons Learned in Preventing Waste, Fraud, and Abuse Implementation Act of 2006 - Amends the Homeland Security Act of 2002 to direct the Secretary of Homeland Security to ensure that: (1) all Department of Homeland Security (DHS) agencies that administer federal emergency assistance maintain internal management controls to detect, prevent, and deter waste, fraud, and abuse; and (2) databases used by DHS to collect information on eligible recipients are integrated with disbursement and payment records to identify ineligible applications.

Requires: (1) the DHS Inspector General to review relevant databases to assess the implementation of internal controls; (2) the Secretary to biennially certify that such controls are in place; (3) entities receiving assistance to periodically report to the disbursing federal agency; (4) the Secretary to implement a waste, fraud, and abuse detection and prevention training program; (5) agencies disbursing assistance to attempt to confirm the applicant's identity and eligibility; and (6) the Small Business Administration (SBA) Administrator to collect, verify, and maintain information regarding applicant eligibility for loans to recover from an emergency.

Directs the Secretary to: (1) require contractors to submit information on performance before awarding, renewing, or extending a contract; and (2) maintain a database of small business entities for federal emergency-related contracting.

Establishes within the Office of Inspector General the position of Deputy Inspector General for Response and Recovery to conduct audits and investigations and to establish a Fraud Task Force. Requires departmental entity heads to maintain budgetary procedures to distinguish funds related to response and relief efforts from other agency funds.