U.S. District Court Judge Timothy Burgess rejected a plea deal for Shawn Christy, 20, and his father, Craig Christy, 48, and instead ordered the men to stand trial in early January.
The plea agreement would have let the two avoid prison time and six-figure fines.
Burgess said the plea agreements prosecutors had reached with the Christys were not acceptable to him. The judge cited what he described as a disturbing pattern of threats.
"They seem undeterred in their conduct," Burgess said.
The Christys were arrested in Pennsylvania in August and are in custody in Anchorage. Prosecutors said the men were upset about state restraining orders issued on behalf of the former Alaska governor and 2008 Republican vice presidential candidate, along with Palin family members and friends.
The restraining orders were issued after Palin left office.
The restraining order against Shawn Christy was issued last year and then renewed earlier this year because he was accused of stalking Palin. The order against Craig Christy was issued in May after he was accused of barraging Palin's parents with antagonizing telephone messages.
The men later acknowledged making harassing phone calls from Pennsylvania to Palin's attorney, John Tiemessen. The Christys reached their plea deals with prosecutors in November.
The state restraining orders against the men have been extended another six months.
Tiemessen, who appeared at Wednesday's hearing, declined to comment.
According to federal court documents, Craig Christy threatened to kill Tiemessen in one obscenity-riddled message and Shawn Christy said he might have sex with Palin in another. Shawn Christy also threatened to come to Alaska and rape one of the attorneys, according to the documents.
The documents say Tiemessen's offices in Anchorage and Fairbanks received hundreds of calls, sometimes in one day, with some of the calls involving threats against Tiemessen and Palin.
Important warning about e-mails purporting to be from the adn.com staff.