The New York Times revealed that informed sources told the newspaper that a senior Justice Department official appointed by Trump ordered an extensive investigation into the Columbia University student protesters over the past few months, sparking anger and concern among prosecutors and investigators who viewed the request as politically motivated and lacking legal basis.

The sources added to the newspaper that the request to investigate students who protested Israel's conduct in the Gaza conflict also drew opposition from a federal judge, who deemed some of the steps sought by the official, Emil Bove III, unjustified and potentially violating the First Amendment to the US Constitution.

The scope of the investigation, conducted by the Justice Department's Civil Rights Division, has not been previously reported. The ensuing dispute highlights the tensions gripping the department as administration officials seek to implement President Trump's agenda. This proposal involves redirecting the Civil Rights Division away from its traditional approach of protecting minority rights to a new mission: fulfilling a campaign promise to crack down on student protesters amid allegations of rampant anti-Semitism on campus.

According to current and former officials, these demands from political appointees at the Justice Department are part of the reason for the exodus of lawyers from the department in recent weeks.

The federal investigation into the student protests at Columbia University appears to have stalled for now, but it represents one of the most contentious episodes so far within the Justice Department during Trump's second term. The people told the newspaper that the dispute has created ongoing ill will within the department, as well as in the courts and the FBI.

When asked for comment, Deputy Attorney General Todd Blanche said, "This is a false story concocted by a group of people who have allowed anti-Semitism and support for Hamas terrorists to fester for years, standing by and doing nothing."

The Trump administration has pledged to address the university protests against Israel's military campaign in the Gaza Strip, saying they reflect anti-Semitism that warrants punishment. These efforts target both college administrators, whom Trump officials say should have done more to curb campus protests, and the student activists themselves, some of whom have been detained by immigration officials. The activists, in turn, accuse authorities of conflating criticism of Israeli and US policies with anti-Semitism.

The investigation began shortly after masked protesters stormed Milbank Hall, a building at Columbia University's Barnard College, on February 26 to demonstrate against the expulsion of students accused of disrupting a Modern Israel History lecture. Video footage shows students shoving a security guard and occupying a hallway. School officials said the guard was assaulted and hospitalized with minor injuries. Boff, a senior Justice Department official, ordered an immediate investigation, primarily into one specific student group, Columbia University Against Apartheid, according to three people familiar with the matter who spoke on the condition of anonymity to discuss details meant to remain confidential.

At Pough's urging, prosecutors in the Civil Rights Division were asked to obtain a list of the group's members. However, investigators rejected this instruction because they were skeptical that such a list existed, given the opaque nature of online forums. Even if it did exist, vetting people's memberships seemed like a potential violation of their First Amendment rights, according to these individuals.

One of the Justice Department lawyers assigned to the case was Samantha Tribble, a seasoned civil rights prosecutor who secured a federal conviction against Derek Chauvin, the Minneapolis police officer who killed George Floyd in 2020, the people said. The people said prosecutors told them that Poff was seeking a list so the information could be shared with immigration agents. The people said prosecutors within the Civil Rights Division feared their criminal investigation could be used to facilitate a Trump administration campaign of intimidation and deportation against student protesters. They added that prosecutors refused to compile such a list that could be provided to Immigration and Customs Enforcement agents. The people said Poff then shifted his focus to obtaining a search warrant for the group's Instagram account. They said they instructed prosecutors to request a search warrant for non-public data associated with the account.

These people said that prosecutors' superiors informed them that Poff was seeking a list so that the information could be shared with immigration agents. These people said that prosecutors within the Civil Rights Division had become concerned that their criminal investigation was being used to facilitate a campaign of intimidation and deportation by the Trump administration against student protesters. They said that prosecutors refused to compile such a list that could be provided to Immigration and Customs Enforcement agents. They added that Poff then shifted his focus to obtaining a search warrant for the group's Instagram account. They said they instructed prosecutors to request a search warrant for non-public data associated with the account. They said the premise of the request was also controversial within the department. Poff insisted that the Instagram account in question had been used to issue a threat, while prosecutors argued that the statement did not meet the legal definition of a threat. In late March, the social media company suspended the group's account for failing to meet its "community standards."

Blanch added in his statement that the search warrant request, which focused on Columbia University's campaign against apartheid, "included an image from CUAD's social media accounts showing the inverted triangle symbol used by Hamas to identify targets of violence, spray-painted on Columbia University property with red paint designed to look like blood."

He said the investigation was "ongoing," apparently referring to a related criminal investigation by federal authorities, which "included an independent judge finding good cause to believe there was evidence of land at Columbia University housing and concealing illegal immigrants."

Before Trump addressed the Justice Department on March 14, Blanch told the audience that the department was investigating whether anyone involved in the Columbia University campus protests violated civil rights and anti-terrorism laws.

Blanche expressed his firm belief in the wisdom of conducting such an investigation. But behind the scenes, the professional lawyers harbored deep doubts about the merits of the case they had been assigned to, and deep fears about the potential consequences of their refusal.

Bove's demands angered staffers in the Civil Rights Division, but many managers were afraid to respond, having watched Bove a month earlier press prosecutors in another division, the Public Integrity Division, to drop criminal charges against New York Mayor Eric Adams, according to the three people. That division, which once had about 30 lawyers, now has only a handful.

Bennett Gershman, a law professor at Pace University who specializes in prosecutorial ethics, told the newspaper that Mr. Bove's described behavior was "astonishing."

“He did something that prosecutors are absolutely prohibited from doing—using government law enforcement powers to attempt to intimidate these individuals or destroy their rights,” Gershman said. “This goes far beyond the bounds of prosecutorial professionalism and adherence to the principles of justice.” In his statement, Blanche said that “the unethical and inaccurate allegations made by deep state terrorist sympathizers, who have stood by as members of the Jewish faith, have been targeted across the country” and will not deter Attorney General Pam Bondi and the Department of Justice from “vigorously investigating criminal conduct and rooting out anti-Semitism.”

When federal prosecutors investigating the student protests applied for a search warrant, a New York magistrate judge denied the request, saying the government lacked sufficient cause, the people said.

In an unusual move, Poff insisted that the plaintiffs appeal the ruling to a district court judge, according to these people. After reviewing the request, Judge John J. Koeltl of the federal court for the Southern District of New York instructed Chief Magistrate Judge Sarah Netborn to reconsider the request, according to these people.

But the second time, the government lawyers' fate was even worse. Judge Netburn not only denied the search warrant request, but also ordered the government to abide by a special condition: If prosecutors try to refile such a request before another federal judge, they must include a transcript of the confidential discussions in her court, according to these people.

Part of the judge's skepticism stems from the absence of lawyers from the Manhattan federal prosecutor's office in the case, these people said. But prosecutors in the Southern District of New York were wary of signing on to the effort and had little role in it, according to these people. A spokesman for the U.S. Attorney's Office in Manhattan declined to comment.

While civil rights prosecutors conducted the investigation Bove requested, they often opposed specific steps he wanted to take, these people said, arguing that they were either not justified by the available facts or conflicted with the law and past practice, or both.

At one point, Bove instructed FBI agents on the New York Joint Terrorism Task Force to don their SWAT vests, go to the Columbia campus, and stand in formation near any protesters. These individuals said the instruction was viewed within the Civil Rights Division as completely inappropriate and a blatant attempt to intimidate students. The FBI agents did not demonstrate any such show of force.

By early April, the investigation appeared to be largely over, but nothing prevented Bove or others from reviving it. But in the aftermath, people familiar with the case said it only exacerbated ill will and mistrust between political appointees at the Justice Department's headquarters in Washington and the New York attorney general's office, as well as between those political appointees and veterans of the Civil Rights Division.