Special Criminal Contempt of Congress Procedures Act of 2009 - Establishes alternate procedures for the prosecution of current or former officers or employees of the executive branch found in contempt of Congress for refusal to testify or produce documents in response to a congressional subpoena. Requires the Speaker of the House of Representatives to certify a finding of contempt of Congress to the appropriate U.S. attorney for presentation to a grand jury. Requires the Chief Judge of a U.S. district court to appoint a special counsel to prosecute any contempt case certified by the Speaker if the Attorney General or U.S. attorney to whom a finding of contempt was certified declines to prosecute or a grand jury does not return an indictment within a specified time period. Requires such special counsel to be an attorney in good standing with substantial prosecutorial experience who did not serve in the administration of a President in office when a finding of contempt was certified. Grants full power and independent authority to the special counsel to exercise all prosecutorial functions and powers.Sets forth provisions for the removal of the special counsel and the termination of the special counsel's authority. Increases the penalty for refusal of witnesses to testify or produce papers in response to a congressional subpoena.Makes this Act effective on January 20, 2009.