Federal Funding Accountability and Transparency Act of 2006 - Directs the Office of Management and Budget (OMB) to ensure the existence and operation of a single updated searchable database website accessible by the public at no cost, that includes for each entity receiving federal funding: (1) the amount of federal funds received in each of the last 10 fiscal years; (2) an itemized breakdown of each transaction; (3) the entity's location and primary location of performance; and (4) a unique identifier for the entity and its parent entity.