Criticism of the government’s management of federal lands in the West isn’t limited to the Sagebrush Rebellion — the Nevada rancher who has refused to pay cattle grazing fees, and his kinfolk leading an armed occupation of a wildlife refuge in Oregon. There’s also a federal judge who has ruled that ranchers with nearby water rights can graze their cattle on federal land without a permit.

At a trial on civil trespassing charges against a Nevada rancher, U.S. District Judge Robert Clive Jones of Reno described Bureau of Land Management officials as “arrogant,” dismissed almost all of the charges, invited the rancher to sue the government, and held two federal officials in contempt of court.

On Friday, a federal appeals court in San Francisco overruled Jones, rebuked him for his comments and ordered him removed from the case.

“Unfortunately, the judge’s bias and prejudgment are a matter of public record,” the Ninth U.S. Circuit Court of Appeals said in an emphatic 3-0 decis ion.

‘Abused power of contempt’

The court said Jones’ ruling — that a rancher who holds water rights from the state can graze cattle within a half mile of the water without a federal permit — ignored appellate law that has been established since 1967.

“An owner of water rights — like all other persons — may graze cattle on federal lands only if he or she has obtained a grazing permit or other grazing authorization,” Judge Susan Graber said in Friday’s ruling. “Water rights are irrelevant to that basic requirement.”

Graber also said Jones “grossly abused the power of contempt” by seeking to punish federal officials who were doing their jobs.

The case isn’t directly related to the campaign against federal land regulation that has become known as the Sagebrush Rebellion. But it illustrates the same conflicts that led to the high-profile standoffs between federal officials and protesters led by Nevada rancher Cliven Bundy .

Bundy has refused to pay $1 million in cattle grazing fees and led a group of supporters who faced off against federal officers in 2014. His son Ammon leads an armed group that has taken over the headquarters of a wildlife refuge in Oregon, protesting federal control of the lands and increased prison sentences for two ranchers convicted of arson on government property. The government has not acted against either group of protesters.

The court case has Sagebrush Rebellion connections. The rancher originally involved in the case, H. Wayne Hage, sympathized with the protest movement and wrote a 1994 book, “Storm Over Rangelands: Private Rights in Federal Lands,” that is popular among its adherents.

Hage held a grazing permit for federal lands, about 200 miles north of Las Vegas, from 1978 until 1993, when the government refused to renew his permit, finding defects in his application. He continued to graze cattle on the land until his death in 2006. The trespass charges run from 2004 to 2008, when the property was managed by his son, also named Wayne Hage.

Dropping trespassing claims

In his ruling in 2013, Jones said the Hages, because they had the right to use water from nearby streams, also had an easement — a right to bring their cattle across public lands, and let them graze, within a reasonable distance of the water, which he defined as a half mile. The judge dismissed all the trespassing claims except two, awarded the government $165.88 in damages, and ordered federal agencies to issue grazing permits to the family.

A property-rights group, the Pacific Legal Foundation, sided with the Hages. Foundation lawyer Brian Hodges said Friday the appeals court had misunderstood Jones’ order, which merely allowed the family to gain access to their state-allotted water, with some “incidental” grazing along the way.

“You can’t stop a cow from putting its head down while you’re driving it to water,” Hodges said.

But the court said Jones had allowed unrestricted grazing on federal lands, without a permit or any support in the law.

Graber said Jones made his attitude clear on the first day of the trial, when he said the Bureau of Land Management displayed “the standard arrogant, arbitrary, capricious attitude that I recognize in many of these cases.”

Other conflicts with court

Jones, appointed to the bench by President George W. Bush in 2003, has had other run-ins with the appeals court.

The court has removed him from several cases, including one in which he refused to allow federal government attorneys from outside Nevada to appear in his court. And when the appeals court ordered Jones in 2014 to allow same-sex couples in Nevada to marry — reversing his 2012 ruling that upheld the state’s ban on same-sex marriages — he instead removed himself from the case.

Graber said appeals court judges have twice suggested scrutiny of Jones’ conduct by the court’s disciplinary body, the Judicial Council.

The council rarely takes public action against a federal judge, and has not done so against Jones. Deborah Rhode, a Stanford law professor who teaches legal ethics, said the council’s general reluctance to act is the downside of a system designed to minimize political influence over federal judges, who are appointed for life and can be removed only by congressional impeachment.

“In order to insure the independence of the judiciary, we’ve insulated them from accountability,” Rhode said.

Bob Egelko is a San Francisco Chronicle staff writer. E-mail: begelko@sfchronicle.com Twitter: @egelko