Federal Bureaucracy Accountability Act of 1999 - Requires a Federal agency and its officers and employees, in civil cases, in administering a statute, rule, regulation, program, or policy (statute) within a judicial circuit, to adhere to the existing precedent respecting the interpretation and application of such statute, as established by the decisions of the U.S. court of appeals for that circuit, with exceptions.

Allows an agency to take a position, either in administration or litigation, that is at variance with such precedent if: (1) it is uncertain whether the administration of the statute will be subject to review exclusively by the appeals court that established that precedent or a court of appeals for another circuit; (2) the Government did not seek further review of the case in which that precedent was first established in that appeals court or the U.S. Supreme Court because neither the United States nor any agency or officer thereof was a party to the case or because the decision establishing that precedent was otherwise substantially favorable to the Government; or (3) it is reasonable to question the continued validity of that precedent in light of a subsequent decision of that appeals court or the U.S. Supreme Court, a subsequent change in any pertinent statute or regulation, or any other subsequent change in the public policy or circumstances on which that precedent was based.