In 1984 the ISDEA was amended.  Section 9 was updated to delete reference to the Federal Grant and Cooperative Agreement Act and to refer to chapter 63 of Title 31 United States Code. In 1987, in another amendment to ISDEA,  language was added respecting personal injury claims resulting from performance of medical and dental functions or studies. In 1988, three amendments to the ISDEA made a great number of changes including amending  its policy statement to emphasize that Congress was committed to supporting and assisting Indian Tribes to develop strong and stable tribal governments. A number of definitions were added and clarified. More specific language was added to clarify record-keeping requirements, etc. Some of the more important changes are discussed below.
A “self-determination contract” was better defined. The declination process was revised to make it much more difficult for the Secretary to decline to contract. The process was formalized to require the Secretary to approve of proposals for self-determination contracts within 90 days of receipt. In order to decline a proposal, the Secretary had to make a specific finding within 60 days of receipt, make his objections known in writing, and provide technical assistance to the Tribe to overcome his objections. The application of Federal procurement laws was limited.
The Administrative Provisions were revised to limit the application of Federal procurement laws to construction contracts executed under new section 102. Federal procurement laws would no longer apply to contracts. Reasonable contract support costs to comply with the terms of the contract and to support prudent management were also added. The Secretary was prohibited from reducing contract-funding amounts due to accrued savings, contract monitoring, or to pay for Federal functions or Federal personnel costs. Contract support costs could be increased. The Secretary was required to provide an annual report to Congress accounting for: contract funding amounts and budget; direct and indirect cost bases, rates, and pools; and deficiencies of funds. Indirect cost shortfalls were prohibited from being used to make adverse adjustments to future year cost rates or funding amounts.
Congress revised Section 107, Promulgation of Rules and Regulations, to require negotiated rulemaking procedures under the Administrative Procedures Act. The Secretary was directed to engage in rulemaking with Indian Tribes within three months and to publish final rules within 10 months of the date of the amendments’ enactment. Under Reassumption of grants, grant recission required that a hearing on the record be held on a date subject to approval by the tribal organization, not the Secretary. United States district court jurisdiction for civil actions and claims against the Secretary was granted. Other changes were made applying: The Federal Tort Claims Liability Act to self-determination contracts; The Equal Access to Justice Act to administrative appeals; and the Contract Disputes Act to contract disputes. Finally, a new Title III was added for a Tribal Self-Governance Demonstration Project with the Department of Interior and Bureau of Indian Affairs that applied to land, services, etc. administered by that department.
Unlike the original Act, the decision to contract was no longer discretionary. A Self-Determination contract was redefined to mean “an intergovernmental contract that is not a procurement contract.”  Existing procurement laws and regulations no longer applied to intergovernmental contracts that were not construction contracts.  Senate Report 100-274 stated:
A fundamental objective of the Federal policy of Indian self-determination is to increase the ability of tribal governments to plan and deliver services appropriate to the needs of tribal members. Consequently, the Indian Self-Determination Act provides Tribes with the flexibility to redesign Federal programs and services to meet the needs of Indian people.  [Emphasis supplied].