Independent Pharmacy Protection Act of 2006

Independent Pharmacy Protection Act of 2006 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act to require each prescription drug plan contract entered into with a plan sponsor to provide for: (1) the availability of direct deposit payments; (2) an increased dispensing fee for generic drugs; and (3) payments within 10 days for certain pharmacies.

Requires the dispensing fee paid to a participating pharmacy for a generic covered part D drug therapeutically equivalent and bioequivalent to a brand name covered part D drug dispensed through the pharmacy to be at least 50% greater than the dispensing fee for the brand name drug.

Limits to $10 the dispensing fee paid to a participating pharmacy for a generic covered part D drug.

Prohibits a prescription drug plan, subject to exception by the Secretary of Health and Human Services, from decreasing the dispensing fee paid to a participating pharmacy for a brand name drug to an amount less than the dispensing fee paid for it on the date of enactment of this Act.

Applies this Act to contracts with a Medicare Advantage organization in the same manner as they apply to those with a prescription drug plan sponsor.