Citizen Petition Fairness and Accuracy Act of 2006

Citizen Petition Fairness and Accuracy Act of 2006 - Amends the Federal Food, Drug, and Cosmetic Act to require that any citizen petition or request for stay of action related to an abbreviated new drug application include a statement that the petition: (1) includes all information and views on which the petitioner relies; (2) is well grounded in fact and warranted by law; (3) is not submitted for an improper purpose; and (4) does not contain a materially false, misleading, or fraudulent statement. Requires the Secretary of Health and Human Services to investigate any petition that does not comply.

Allows the Secretary to impose penalties for knowingly and willfully submitting a petition for an improper purpose or that contains a materially false, misleading, or fraudulent statement. Provides that such penalties may include: (1) civil penalty; (2) suspension or revocation of the authority to submit a petition; and (3) dismissal of the petition. Requires the Secretary to refer such a violative petition to the Federal Trade Commission (FTC) for further action. Sets forth the factors that the Secretary shall consider in taking an enforcement action or determining the penalty.

Permits any person aggrieved by a petition that may contain violations to request the Secretary to investigate. Subjects knowing and intentional violative requests to civil penalties.

Requires the Secretary to take final agency action on such a petition within six months.