Medicare Physician Payment Reform and Quality Improvement Act of 2006

Medicare Physician Payment Reform and Quality Improvement Act of 2006 - Amends title XVIII (Medicare) of the Social Security Act (SSA) to revise physician payment requirements under the Medicare program, including the physician payment update and quality measures for physicians' services.

Terminates application of the sustainable growth rate (SGR), replacing it with a single conversion factor, the Medicare economic index (MEI) minus 1%.

Requires the Secretary of Health and Human Services to provide for the selection of quality performance measures (Q-measures) for assessing physician, non-physician practitioner, and supplier services and determining ratings for them. Requires such Q-measures to be developed in conjunction with physician specialty organizations and consensus-building organizations.

Eliminates specified limitations on the balance billing of highest income beneficiaries.

Revises requirements for the quality improvement program (QIO), including program administration, data disclosure, use of evaluation and competition, quality improvement funding, and qualifications for QIOs under part B (Peer Review) of SSA title XI.

Amends SSA title XIX (Medicaid) to permit alternative quality improvement programs under such program.

Terminates the availability of funds from the MA Regional Plan Stabilization Fund.

Directs the Board of Trustees of the Federal Hospital Insurance Trust Fund and of the Federal Supplementary Medical Insurance Trust Fund to monitor and examine the extent to which the different Medicare funding mechanisms provide an appropriate alignment with the program goals of the respective parts.

Provides for a one-year delay in Medicare adjustments in payments for imaging services.

Eliminates the three-year phase-in for implementation of the reduction in Medicare part B premium subsidies for higher income beneficiaries (thus requiring immediate application of the reduction adjustment).