Medicare Physician Payment Reform Amendments of 1989 - Amends part B (Supplementary Medical Insurance) of title XVIII (Medicare) of the Social Security Act to phase-in, from 1990 to 1993, Medicare payment for physician services pursuant to a fee schedule which is based upon the relative value of the resources devoted to each physician service. Directs the Secretary of Health and Human Services to adjust fee schedule amounts to take into account geographical variations in resource values and to make the transition to such payment methodology budget neutral.

Prohibits the Secretary, after 1990, from making variations in the relative value of a physician service turn on whether the physician is a specialist or such service is his or her specialty.

Requires that, after 1991, classification and coding of physician services: (1) be uniform for the same physician service in all fee schedule areas; (2) include pre-operative and post-operative physician services with related surgical procedures; and (3) differentiate evaluation and management services (primary case) on the basis of the time spent in providing different primary care services.

Directs the Secretary to report to the Congress, by July 1, 1991, on whether geographical variations in fee schedules should be based on variations in resource values among States or between urban and rural areas.

Factors malpractice expenses into the relative value of a physician service.

Phases-in, from 1991 to 1993, the limitation of a nonparticipating physician's actual charge for a service to 120 percent of the fee schedule amount for such service.