A federal judge this week dismissed charges against nearly 100 migrants detained under a Trump administration effort to arrest undocumented migrants for trespassing on a newly declared “national defense” zone along New Mexico’s border with Mexico.

The order from a federal magistrate judge, Gregory B. Wormuth, added to the confusion and legal turmoil that have gripped New Mexico in the month since President Trump declared a ribbon of land along the 180-mile length of the state’s southern border to be an Army base.

Around 400 migrants had been charged with willfully violating security regulations — misdemeanor charges that can carry up to a year in jail. The arrests, which Defense Secretary Pete Hegseth was praising just last Friday, had swamped local jails and every day brought dozens of shackled migrants into a federal courtroom to face the novel charges.

“When you cross illegally, you will be prosecuted to the fullest extent of the law,” Mr. Hegseth said in a social-media message.

But Judge Wormuth, a former federal prosecutor, said the federal government had failed to show that the migrants actually knew they were unlawfully entering a restricted military area. He has dismissed charges against 98 migrants so far as he works through the docket.

“The United States provides no facts from which one could reasonably conclude that the Defendant knew he was entering” the New Mexico National Defense Area, the newly declared military installation, Judge Wormuth ruled.