Fairness and Transparency in Contracting Act of 2009

Fairness and Transparency in Contracting Act of 2009 - Amends the Small Business Act to exclude as a small business, for purposes of meeting federal agency contracting goals with small businesses, any small business (or subsidiary thereof) that is publicly traded, or any business (or subsidiary thereof) with more than 50% non-U.S. citizen ownership. Requires the Administrator of the Small Business Administration (SBA) to notify the head of each federal department or agency regarding this Act and its amendments, and the department or agency head to then notify its contractors.

Directs the Administrator to: (1) publish a report regarding federal prime contracts awarded to businesses identified as small businesses for purposes of achieving small business contracting goals; and (2) establish procedures to ensure that the Central Contractor Registration database provides an adequate warning regarding criminal penalties for misrepresenting the status of a small business or person in order to obtain federal contracts.

Provides for enforcement of complaints about the classification of a business for such purposes.