Medicare Prescription Drug Emergency Guarantee Act of 2006

Medicare Prescription Drug Emergency Guarantee Act of 2006 - Amends part D (Voluntary Prescription Drug Benefit Program) of title XVIII (Medicare) of the Social Security Act (SSA) to assure uninterrupted access to medicines under the Medicare prescription drug program.

Requires each prescription drug plan sponsor offering a prescription drug plan, and each Medicare Advantage organization offering an Medicare Advantage-Prescription Drug Plan (MA-PD plan), to: (1) provide minimum standard transition coverage; (2) furnish each enrollee with annual notices of any changes in formulary or other restrictions or drug coverage limitations; and (3) require application of intermediate sanctions to protect against fraud and abuse.

Amends SSA: (1) title XVIII part C (Medicare+Choice) to allow changes of enrollment in prescription drug plans and MA-PD plans to be made once each year outside the annual coordinated election period, or twice a year; and (2) title XIX (Medicaid) to prohibit conditioning Medicaid eligibility on enrollment in Medicare part D or any other creditable coverage.

Directs the Medicare Payment Advisory Commission (MEDPAC) to study and report to Congress on the extent to which full-benefit dual eligible individuals were enrolled (by assignment or otherwise) in the most appropriate part D prescription drug plans.

Directs the Secretary of Health and Human Services to reimburse covered third parties during 2006 for 100% of covered part D drugs which a prescription drug plan or MA-PD plan enrollee reasonably expected would have been covered but were not because the enrollee was unable to access on a timely basis prescription drug benefits to which he or she was entitled. Directs the Secretary to establish a process for recovering such reimbursed costs from prescription drug plans and MA-PD plans if they should have incurred them.