Federal Election Administration Act of 2006 - Amends the Federal Election Campaign Act of 1971 to replace the Federal Election Commission with the Federal Election Administration (FEA) as an independent establishment to enforce federal campaign finance laws.
Requires enforcement proceedings for violations of campaign finance laws to be conducted before administrative law judges. Allows any final determination made by an administrative law judge to be appealed to the FEA for final agency action, subject to judicial review. Authorizes the FEA to impose civil penalties, issue cease-and-desist orders, and report apparent criminal violations to the appropriate law enforcement authorities. Allows the FEA to conduct audits and field examinations of campaign committees. Prescribes criminal penalties for violations.
Directs the Comptroller General to examine and report to Congress on the Attorney General's enforcement of the criminal provisions of federal campaign finance laws.