Authorities arrested the standoff's leaders on a remote road outside Malheur National Wildlife Refuge on January 26.
With four occupiers refusing to leave since then, authorities have surrounded the refuge and indicted the holdouts but have not forced them to leave.
He is the son of Cliven Bundy, a Nevada rancher who has been involved in a high-profile dispute over grazing cattle on federal land in that state.
Critics say the wait-it-out strategy sends a mixed message and can embolden others to lead takeovers.
"Taking over the refuge was not only right, it was the duty of the people to do", Bundy said. At least 11 militants, including Bundy and his brother, Ryan, are being held without bail; another militant, LaVoy Finicum, was killed in last Tuesday's arrest operation.
The indictment, by a grand jury convened in United States District Court in Portland, comes more than a week after Bundy and others were arrested during a traffic stop three weeks into their armed occupation of the almost 200,000-acre Malheur National Wildlife Refuge in the high desert of eastern Oregon.
In a graphic look at the confrontation between police and armed occupiers in OR, newly released Federal Bureau of Investigation video shows the shooting death of LaVoy F...
It also says the protesters recruited others in person and over social media to join their ranks beginning in November, and, in October, warned the sheriff of Harney County in the nearby town of Burns of "extreme civil unrest" if their demands were unmet, among other acts of intimidation. "This is what you get when government officials ignore the people", Bundy said.
Four holdouts still remain at the occupation of federal buildings.
"No specific threats or incidents have occurred, but we remain vigilant to ensure employee and visitor safety throughout the region", Jody Holzworth, regional spokeswoman for the U.S. Fish and Wildlife Service, said in an email to CBS News.
The indictment, returned by a federal grand jury in Portland on Wednesday and unsealed on Thursday, supersedes an earlier criminal complaint in the case.
The additional security measures are in place at the Klamath Basin National Wildlife Refuge Complex, which straddles the Oregon-California border; Ash Meadows National Wildlife Refuge in Nevada; and Modoc National Wildlife Refuge in Northern California.