Refuge System Protection Act This bill authorizes the Department of Justice (DOJ), at the request of the Department of the Interior, to bring in a district court a civil action against any individual or entity that destroys, causes the loss of, causes Interior to make risk mitigation efforts with respect to, or injures any resource that is within the boundaries of any land or water that is managed by the U.S. Fish and Wildlife Service. The bill also authorizes DOJ, at the request of Interior, to bring in a district court an in rem action against any instrumentality (e.g., a vessel, vehicle, or aircraft) that destroys, causes the loss of, causes Interior to make risk mitigation efforts with respect to, or injures any such system resource. Among others, it shall be an affirmative defense in either type of action that the destruction of, loss of, risk mitigation regarding, or injury to a system resource was caused by an otherwise legal act or omission that occurred outside the boundaries of the resource. In either type of action, the court may award response costs and damages.