Indian Programs Reform Act of 1990

Indian Programs Reform Act of 1990 - Transfers to the Minerals Management Service of the Department of the Interior the functions performed by: (1) the Bureau of Indian Affairs with respect to the distribution of royalty income to Indian tribes and allottees; and (2) Bureau of Land Management with respect to lease enforcement and inspection pertaining to oil and gas leases on Indian lands.

Mandates that purchasers of oil or natural gas from Federal or Indian lands submit prescribed removal forms and annual reports to the Secretary of the Interior (the Secretary). Sets forth civil and criminal penalties for non-compliance.

Directs the Secretary to establish guidelines for the maintenance and inspection of on-site meters used to gauge the production and purchase of oil and natural gas on Federal and Indian lands.

Requires the Director of the Federal Bureau of Investigation in conjunction with the Secretary to create a joint working group to provide training and coordination between the Bureau and the Department with respect to investigations of natural and resource thefts from Federal and Indian lands.

Amends the Federal Oil and Gas Royalty Management Act of 1982 to: (1) increase civil penalties for non-compliance with its terms; and (2) authorize the Secretary to cancel a lease for failure to pay royalties within a specified deadline. Authorizes the Secretary to: (1) conduct audits and impose recordkeeping requirements beyond the current six-year statutory period; and (2) compensate Indian tribes or certain organizations of Indian allottees for the costs incurred in participating in a cooperative agreement under the Act. Extends coverage of such Act to natural resources other than oil and natural gas.

Requires the Minerals Management Service to print annual statistics regarding the auditing of Indian tribal and allottee leases and the frequency of underpayments.