Rural Medical Assistance Facilities Act of 1989 - Directs the Administrator of the Health Care Financing Administration to make ten to 15 four-year grants to no more than six States covering 90 percent of the costs of transforming a rural hospital into a medical assistance facility. Amends the Omnibus Budget Reconciliation Act of 1987 to use funds authorized for the rural health care transition grant program for rural hospital transformation grants.

Amends title XVIII (Medicare) of the Social Security Act to cover services provided by medical assistance facilities. Requires that such facilities: (1) be located in rural areas at least 30 miles from a hospital; (2) provide emergency care, stabilization care, and basic inpatient care for stays not exceeding four days; (3) provide ambulatory care in accordance with standards to be established by the Secretary; (4) receive quality assurance and utilization review services; (5) agree to participate in the Medicaid program (title XIX of the Act); and (6) have transfer and discharge planning agreements with referral hospitals. Authorizes such facilities to provide obstetric services and outpatient surgical care pursuant to protocols to be established by the Secretary.

Makes Medicare rural hospital staffing requirements applicable to medical assistance facilities, but authorizes facility care to be provided by nurse practitioners or physician assistants pursuant to protocols developed by the Secretary so that such facilities have flexibility in meeting physician "on call" requirements. Exempts such facilities from hospital 24-hour service requirements.

Authorizes the Secretary to develop a methodology for reimbursing medical assistance facilities which differs from that used in reimbursing hospitals.

Amends the Medicaid program to cover services provided by medical assistance facilities.

Sets forth reporting requirements.