Boundary Waters Canoe Area Wilderness Accessibility and Partnership Act of 1996 - Modifies certain restrictions on motorboat use on specified lakes within the Boundary Waters Canoe Area Wilderness, Minnesota.

Permits the operation of motorized vehicles and associated equipment to assist in the transport of a boat across the portages from the Moose Lake Chain (currently, Sucker Lake) to Basswood Lake, from Fall Lake to Basswood Lake, and from Lake Vermilion to Trout Lake.

Establishes the Boundary Waters Canoe Area Wilderness Intergovernmental Council to develop, review, monitor implementation of, and, if necessary, modify a comprehensive management plan for the Wilderness. Prohibits the Council from considering: (1) removing the wilderness designation; (2) allowing mining, logging, or commercial or residential development; or (3) allowing motorized uses not otherwise authorized.

Provides for review, recommendations for revisions, and approval or disapproval of such plan by the Secretary of Agriculture.

Prohibits the Secretary, pending approval of the plan, from issuing any regulation that relates to the Wilderness, except for: (1) regulations required for routine business, such as issuing permits, visitor education, maintenance, and law enforcement; and (2) emergency regulations.