Medicare Controlled Substances Accountability Act of 1990 - Amends part A (Hospital Insurance) of title XVIII (Medicare) of the Social Security Act to cut Medicare payments under part A for inpatient hospital and extended care services provided in a State by one-half if the State does not implement a controlled substance accountable prescription system.

Requires that such system: (1) prohibit a health care practitioner from prescribing certain controlled substances without writing the prescription on a form, provided by the State, which identifies such practitioner; and (2) require such practitioner to maintain a readily retrievable record of such transactions. Requires every person who dispenses such controlled substances to maintain a two-year record of such transactions, including the information contained on prescription forms, and provide information in such record to the State at least every two months.

Makes the system inapplicable to drugs dispensed directly by a practitioner to a user and drugs dispensed by oral prescription in emergency situations. Limits the use of system information to the enforcement of laws under the Medicare program, title XIX (Medicaid) of the Social Security Act, the Controlled Substances Act, or a State controlled substances Act. Requires States and the Secretary of Health and Human Services to maintain active programs to process system information and investigate potential violations of law identified by such information.