Medicare Specialty Care Improvement and Protection Act of 2009

Medicare Specialty Care Improvement and Protection Act of 2009 - Amends part C (Medicare+Choice) of title XVIII (Medicare) of the Social Security Act (SSA) to extend through December 31, 2013, the authority to restrict enrollment for specialized Medicare Advantage (MA) plans for special needs individuals (SNPs).

Extends such authority through December 31, 2015, in the case of a SNP designated as a Fully Integrated Dual Eligible Special Needs Plan..

Directs the Secretary of Health and Human Services (HHS) to evaluate the MA and the health status risk adjustment payment mechanisms in order to resolve plan payment inequities relative to Medicare fee-for-service payments for high-risk, high cost beneficiaries. Directs the Secretary, using the results of the evaluation, to refine the risk adjustment payment mechanism for such beneficiaries.

Requires the Secretary to provide bonus payments to account for added SNP costs associated with additional benefit, care management, reporting, and other requirements established by Congress and the Secretary in excess of other MA plans.

Requires the Secretary to take into account specified factors, including dual eligibility (for both Medicare and SSA title XIX [Medicaid] benefits) and geographic cost differences, with respect to the bid structure for SNPs.

Requires the Secretary to have in place a process under which the Secretary designates dual eligible SNPs as Fully Integrated Dual Eligible Special Needs Plans for the purpose of advancing fully integrated Medicare and Medicaid benefits and services for dual eligible beneficiaries, including state-designated Dual subsets.

Directs the Secretary to establish or designate an Office on Medicare/Medicaid Integration.

Authorizes a plan, at state option, to provide for a period of presumptive eligibility for an individual who has attained age 65, who has 12 or more consecutive months of Medicaid eligibility, and who the state has reason to believe will be determined to be a full-benefit dual eligible individual.

Conditions such presumptive eligibility, however, on the state's: (1) agreement to randomly conducted eligibility audits by the Secretary; and (2) ensuring that any individual enrolled under the state plan who is determined ineligible for medical assistance as a result of such an audit is notified at least 30 days before disenrollment.

Extends prescription drug discounts to enrollees of Medicaid managed care organizations.