Medicare Prescription Drug Integrity Act of 2013 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act (SSA) to require a prescription drug plan (PDP) sponsor to have in place procedures designed to prevent fraud and abuse in PDPs.

Authorizes the Secretary of Health and Human Services (HHS), with respect to establishing special enrollment periods for full-benefit dual eligible individuals, to set coverage limits for individuals who have obtained coverage for a covered Medicare part D drug at a frequency or amount not medically necessary.

Amends SSA title IX to allow the Secretary to exclude from participation in any federal health care program any individual or entity that has engaged in the inappropriate prescribing or dispensing of a covered Medicare part D drug.

Amends SSA title XVIII part D to allow a PDP or a MedicareAdvantage-PD (MA-PD) plan to exclude from qualified prescription drug coverage, and deny payment for, any covered part D drug: (1) prescribed or dispensed inappropriately to an individual under a PDP or a MA-PD plan that could not have been prescribed or dispensed to the individual on the date of such prescribing or dispensing; or (2) any drug at a frequency or amount that represents a practice or pattern of abusive prescribing or dispensing, or presents a risk to enrollee health or safety.

Amends the Controlled Substances Act to direct the Attorney General to: (1) compile a list of the unique health identifiers of prescribers and dispensers that are members of a group practice registered and authorized to prescribe or dispense controlled substances in schedules II and III, and (2) make the list available to all PDP sponsors.

Amends SSA title XVIII with respect to the use of recovery audit contractors under the Medicare Integrity Program to identify underpayments and overpayments and recoup the latter. Authorizes the Secretary to retain an additional portion of up to 25% of the amounts recovered for purposes of carrying out this Act.