Intergovernmental Tax Agreement Act of 1999

Intergovernmental Tax Agreement Act of 1999 - Grants U.S. consent to States and Indian tribes to enter into intergovernmental compacts and agreements concerning the collection and remittance of : (1) applicable State taxes on retail commercial transactions involving non-Indians on Indian lands; or (2) covered tribal equivalency taxes.

Permits: (1) a tribe to request the Secretary of the Interior to initiate negotiations on that tribe's part with a State for the purpose of entering into a tax compact; and (2) a State to request the Secretary to initiate negotiations between a tribe and the State to enter into such a tax compact.

Requires: (1) a request by a tribe or State to be in writing; (2) the Secretary to issue a written response within 30 days after receiving a request to the submitting tribe or State; (3) the Secretary to commence negotiations with respect to the tax compact that is the subject of the request submitted by the tribe or State within 30 days after receiving such request; and (4) the parties to complete the negotiations within 120 days, unless the parties agree to an extension.

Directs the Secretary to initiate a mediation process, with the goal of achieving a tax compact, if: (1) the party that was requested to enter into negotiations failed to respond to that request; or (2) upon the completion of an applicable period for negotiations, the parties have failed to execute a compact.

Establishes an Intergovernmental Dispute Resolution Panel to consider and render decision on: (1) a dispute between a State and a tribe that is referred to the Panel at the Secretary's discretion if negotiations and mediation do not result in the execution of a compact; and (2) any claim involving the collection or payment of retail taxes claimed by a State with respect to transactions conducted on Indian lands.

Grants, except as provided, original jurisdiction to U.S. district courts with respect to: (1) the enforcement of any compact; and (2) any civil action, claim, counterclaim, or setoff brought by any party to secure equitable relief, including injunctive and declaratory relief. Prohibits any action from being brought to recover damages arising out of or in connection with an agreement or compact, except as specifically provided for in that agreement or compact. Provides for each compact to specify that each party to the compact: (1) consents to litigation to enforce the compact; and (2) waives any defense of sovereign immunity to the extent necessary to enforce that compact.