Native American Burial Sites and Cultural Resources Protection Act This bill directs the U.S. Army Corps of Engineers (USACE) to establish a pilot program to protect Native American burial sites, village sites, and cultural resources identified or discovered at covered civil works projects in the watershed of the Sacramento River and its tributaries, including the American, Bear, Yuba, and Feather Rivers, in California. In carrying out this pilot program, USACE must identify, and cooperate with appropriate government property owners to set aside, areas that may be used for the reburial of Native American human remains and funerary objects that have been identified or discovered at the site of a covered civil works project that is being constructed, reconstructed, or repaired, or operated and maintained, using federal funds; have been rightfully claimed by any affected Indian tribe; and can be reburied in a manner secure from future disturbances.