Northern Rockies Ecosystem Protection Act

Northern Rockies Ecosystem Protection Act - Designates the following lands in Idaho, Montana, Oregon, Washington, and Wyoming as wilderness and components of the National Wilderness Preservation System (System): (1) Greater Glacier/Northern Continental Divide ecosystem; (2) Greater Yellowstone ecosystem; (3) Greater Salmon/Selway ecosystem; (4) Greater Cabinet/Yaak/Selkirk ecosystem; (5) Islands in the Sky Wilderness; and (6) Blackfeet Wilderness.

Designates: (1) specified wild land areas as Biological Connecting Corridors to protect the life flow of the Northern Rockies Bioregion; (2) the inventoried roadless areas identified as part of the Corridors as components of the System; and (3) certain biological connecting corridors as special corridor management areas.

Establishes the Hells Canyon/Chief Joseph National Park and Preserve as a National Park System unit. Repeals Federal law provisions that establish the Hells Canyon National Recreation Area.

Requires the Secretary of the Interior to: (1) implement a program of ecosystem restoration in the Preserve; and (2) study the feasibility of creating a Flathead National Park and Preserve in the area generally known as the Glacier View Ranger District of the Flathead National Forest.

Amends the Wild and Scenic Rivers Act to designate segments of specified rivers and creeks in Idaho, Montana, and Wyoming as components of the National Wild and Scenic Rivers System.

Establishes the National Wildland Restoration and Recovery System and the National Wildland Recovery Corps.

Requires the Secretaries of the Interior and Agriculture to assure nonexclusive access to the specified areas and corridors designated by this Act by Native Americans for traditional cultural and religious purposes.