Federal Funding Accountability and Transparency Act of 2006 - Directs the Office of Management and Budget (OMB), by January 1, 2008, to ensure the existence and operation of a single searchable website accessible by the public at no cost that includes for each federal award of federal financial assistance and expenditures (excluding individual transactions below $25,000 and credit card transactions before October 1, 2008): (1) the amount; (2) information including transaction type, funding agency, the North American Industry Classification System code or Catalog of Federal Domestic Assistance number, program source, and an award title descriptive of the purpose of each funding action; (3) the name and location of the recipient and the primary location of performance; and (4) a unique identifier of the recipient and any parent entity.

Requires the website to include data for FY2007 and each fiscal year thereafter. Authorizes the Director of OMB to designate federal agencies to participate in the development, establishment, operation, and support of the website.

Provides that the website: (1) may use as the source of its data the Federal Procurement Data System, Federal Assistance Award Data System, and Grants.gov, if all of these sources are searchable through the website and can be accessed in a search as prescribed under this Act; (2) shall not be considered in compliance if it hyperlinks to websites so that the information elements required in this Act cannot be searched electronically by field in a single search; (3) shall provide an opportunity for the public to provide input about the utility of the site and recommendations for improvements; (4) shall be updated not later than 30 days after issuance of any federal award requiring a posting; and (5) shall provide for separate searches that distinguish between awards that are grants, subgrants, loans, cooperative agreements, and other forms of financial assistance and awards that are contracts, subcontracts, purchase orders, task orders, and delivery orders.

 Requires the Director, by July 1, 2007, to commence a pilot program to: (1) test the collection and accession of data about subgrants and subcontracts; and (2) determine how to implement a subaward reporting program across the federal government. Terminates the pilot program by January 1, 2009.

Requires the Director, by January 1, 2009 (subject to an 18-month extension if compliance would impose an undue burden), to ensure that: (1) data regarding subawards is disclosed in the same manner as data regarding other federal awards under this Act; and (2) the method for collecting and distributing subawards data minimizes burdens imposed on federal award and subaward recipients, allows such recipients to allocate reasonable costs for data collection and reporting as indirect costs, and establishes cost-effective requirements for collecting subaward data under block grants, formula grants, and other types of assistance to state and local governments. Exempts any entity that demonstrates that its gross income did not exceed $300,000 in the previous tax year from the requirement to report subawards until the Director determines that the imposition of such requirement will not cause an undue burden.

Requires the Director to report annually to Congress regarding website implementation and make each report submitted publicly available on the website.

States that nothing in this Act shall prohibit OMB from including through the website access to data that is publicly available in any other federal database or require the disclosure of classified information.

Requires the Comptroller General to submit to Congress a report on compliance with this Act by January 1, 2010.
Output: A bill to require full disclosure of all entities and organizations receiving Federal funds.