Medicare Payment Rate Disclosure Act of 2006 - Amends title XVIII (Medicare) of the Social Security Act to direct the Secretary of Health and Human Services to make publicly available on the official Medicare Internet site: (1) payment rates for hospital inpatient procedures, outpatient procedures, and physicians' services; (2) the period for which payment rates are applicable; (3) services included in certain procedures; and (4) a statement that the average payment rates and average payment amounts are only applicable to the Medicare program and may not be available for an individual who is not purchasing such a procedure or service under the Medicare program.