PORTLAND — Less than two weeks after the armed occupation of an Oregon wildlife refuge ended, people charged with seizing the federal facility pleaded not guilty on Wednesday.

But even as the focus has shifted to the courtroom, with some of the people indicted for the occupation appearing here for an arraignment Wednesday, authorities say that other people could soon be charged for the weeks-long takeover of the Malheur National Wildlife Refuge.

So far, 25 people have been indicted for the Oregon wildlife occupation — 16 of them earlier this month and another nine not long after. Some of these people have also separately been charged for the armed standoff at Cliven Bundy’s Nevada ranch in 2014.

Early next month, the government is likely to file a superseding indictment “that may add additional charges and defendants,” according to a court filing this week from federal prosecutors. It is also possible additional indictments could follow that based on what investigators find as they process evidence, the filing said.

On Wednesday, eight people already charged with the occupation appeared in a federal courtroom, while others sent representatives in their place.

Each of them entered a plea of not guilty, and then several expressed concern about being kept behind bars if they were innocent until proven guilty. One occupier, Ryan Payne, said he has been “led around in chains and shackles everywhere I go.”

Jason Patrick, another occupier, told District Judge Anna J. Brown: “You’re the federal government and you’ll do whatever you want.” The comment drew a shout of “That’s right” from one of the spectators who filled every seat in the court’s benches. The family of Victoria Sharp, who was with some of the occupation’s leaders when they were arrested, sang religious hymns while waiting in the line into the courtroom.

The FBI said a day earlier they were done going through the refuge to check for explosives and any stragglers who may have stayed behind. The refuge has been turned back over to the U.S. Fish and Wildlife Service, but it won’t reopen just yet, authorities say. First, attorneys for the people who have been charged with the occupation will be able to visit the site.

Federal agents going through the sprawling refuge found explosives, firearms and “significant amounts of human feces,” according to a filing last week from the U.S. attorney for the District of Oregon.

They also found evidence that occupiers had a camping area “adjacent to or on a particularly sensitive cultural site” and cleared trenches and created a road on or near “grounds containing sensitive artifacts,” the filing stated.

Agents trained in dealing with crimes related to art and cultural property were involved in the sweep of the refuge, which is the historical home to the Burns Paiute Tribe. Thousands of tribal artifacts are at the site.

An armed group seized the refuge Jan. 2 in support of two local ranchers convicted of arson; the group went on to say they were fighting the federal government’s management of federal lands. The occupation’s leaders were arrested last month while traveling on a highway outside the refuge, and four holdouts remained for another two weeks before they surrendered to authorities. All told, the siege lasted for 41 days.

During the 12 days that the FBI collected evidence at Malheur, agents recovered computers and other electronic devices and checked through the refuge to make sure no other occupiers hung behind after the final holdouts surrendered Feb. 11.

In filings this week, the office of Billy J. Williams, the U.S. attorney for Oregon, proposed that the refuge be opened on Thursday and Friday to “defense attorneys and investigators” for the occupiers who have been indicted.

Prosecutors said in a different filing that “the crime scene in this case is singularly unique,” owing to the size of the refuge. In a proposal outlined Wednesday, Williams’s office says that these attorneys and investigators would be accompanied by federal law enforcement officials and allowed to take photos and video, but not “remove or disturb any items.”

Williams also said authorities would begin restoring the refuge and preparing it to be reopened to the public after the visit from these attorneys.

The attorneys representing some occupiers, though, protested Wednesday in court that they were not being given enough time to view evidence at the refuge.

Lissa Casey, who is defending Ammon Bundy, the occupation’s leader, also pointed out that this plan means attorneys for the occupiers would not be able to return to the refuge later if a new indictment is filed based on evidence found at the refuge,

“I can’t anticipate theoretical issues,” Brown said in response. When Bundy stood to protest, the otherwise affable Judge Brown became stern: “Sit down, sir!” Bundy complied.

Casey also asked to let marshals take Bundy to the refuge so he could personally show his attorneys the relevant evidence at the wildlife refuge. This request was denied.

Brown took issue with the lack of a new indictment by the government, asking federal prosecutors, “When is the government going to have this new indictment?”

One of the prosecutors said it could take as long as three months for the government to file two superseding indictments, including one addressing the volume of evidence being processed by the FBI.

Brown called this length of time “beyond belief,” saying that if additional charges are planned, they should be filed “promptly.”

While prosecutors have filed motions for a trial to be pushed back to next year, Brown said she does not intend to see that happen.

“I am trying very hard to find ways to move this forward,” she said. Brown emphasized a trial date of April 29, though a previous judge had set that date for April 19.

She also discouraged defense attorneys from filing separate motions, saying they had to work together to keep the process moving along.

“Every time a motion is filed, that speedy trial stops,” she said.

An attorney for Peter Santilli, who was charged with the occupation but who says he was there as a journalist, asked for another hearing to review his detention. Brown set that for next week.

It will still take months for forensic teams to analyze all of the evidence that was collected, said Greg Bretzing, special agent in charge of the FBI’s Portland division. In a statement, Bretzing said the FBI returning control of the facility to the Fish and Wildlife Service could “bring some sense of closure to this chapter of the story.”

Berman reported from Washington.


[This story has been updated. First published: 1:33 p.m.]