A judge on Monday largely barred federal agents from making arrests in immigration courts in New York City, putting an abrupt halt to a policy that emerged last year as the centerpiece of the Trump administration’s immigration crackdown in Manhattan.

The federal judge, P. Kevin Castel, issued the ruling two months after the Manhattan U.S. attorney’s office sent a highly unusual letter to the court saying that it had mistakenly relied on a Department of Homeland Security policy memo when detaining noncitizens in immigration court.

Opponents of the Trump administration, including Brad Lander, the former comptroller of New York City who is running for Congress as a Democrat, said the letter amounted to an admission of a “bombshell lie” that had been used as a rationale for the detention of thousands of immigrants.

The policy had led to remarkable scenes within the immigration courts at 26 Federal Plaza in downtown Manhattan, as immigrants attending court for routine hearings were suddenly detained and, sometimes, dragged away from their families. Protesters began to attend in droves and some — including Mr. Lander — were arrested alongside the immigrants.

Lawyers for two nonprofit immigrant advocacy groups, the Door and African Communities Together, had argued against the constitutionality of the courthouse arrests. They called on the judge to stop the policy, which left immigrants scared to attend hearings for fear of being detained.

Federal officials had defended the arrests, saying they allowed agents a safer environment in which to detain their targets, allowing them to avoid the risks of deploying teams into local communities.