Medicare Rural Health Provider Payment Extension Act of 2006

Medicare Rural Health Provider Payment Extension Act of 2006 - Amends title XVIII (Medicare) of the Social Security Act (SSA), as amended by the Deficit Reduction Act of 2005, to extend through calendar 2009 the Medicare rural hospital hold harmless provision under the prospective payment system for hospital outpatient department services.

Amends SSA title XVIII to extend through calendar 2010: (1) the Medicare incentive payment program for physician scarcity areas; (2) Medicare increased payments for ground ambulance services in rural areas; and (3) the floor on Medicare work adjustment.

Amends the Medicare Prescription Drug, Improvement, and Modernization Act of 2003 to extend through July 1, 2011, Medicare reasonable costs payments for certain clinical diagnostic laboratory tests furnished to hospital patients in certain rural areas.

Amends the Medicare Prescription Drug Improvement, and Modernization Act of 2003, as amended by the Deficit Reduction Act of 2005, to extend through calendar 2011 the temporary Medicare payment increase for home health services furnished in a rural area.