Medicare Pharmacy Transparency and Fair Auditing Act - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act to require each contract entered into with a prescription drug plan (PDP) sponsor for the offering of a prescription drug plan to prohibit the PDP sponsor from contracting with any pharmacy benefits manager (PBM) to manage the prescription drug coverage under such plan, or to control the costs of such coverage, unless the manager satisfies specified PBM audit and disclosure requirements.