National Trails System Act Amendments of 1994 - Expresses the sense of the Congress that in order to address problems resulting from the multijurisdictional nature of governmental authority concerning the protection of national scenic and historic trails, the head of each Federal agency with jurisdiction over such trails should: (1) cooperate with States, political subdivisions, and private persons with an interest in the trails to pursue trail development; and (2) be granted authority to protect lands critical to the completion of such trails.

Amends the National Trails System Act to prohibit the Federal Government from acquiring, without the consent of the owner, any land or interest in land outside of the exterior boundaries of any federally administered area for the Potomac Heritage Trail. Places the same condition on the acquisition of lands or interests for the Nez Perce National Historic Trail (from Oregon to Montana).

Prohibits funds from being expended for the acquisition of land or interests outside existing Federal lands for the Continental Divide National Scenic Trail, the North Country National Scenic Trail, the Ice Age National Scenic Trail, the Oregon National Historic Trail, the Mormon Pioneer National Historic Trail, the Lewis and Clark National Historic Trail, or the Iditarod National Historic Trail except with the consent of the owner of the lands or interests. (Current law prohibits funds from being expended for such purposes without such exception.)