The superintendent of the Des Moines Public Schools system will submit his resignation on Tuesday, his lawyer said, days after federal immigration agents arrested him and accused him of living and working illegally in the United States.

The letter of resignation was made public just before the Justice Department announced that it was opening an investigation into whether the Des Moines school system engages in discriminatory hiring practices. In announcing the investigation, federal officials raised concerns about the district’s affirmative action goals and framed the investigation as part of the Trump administration’s broader campaign against diversity, equity and inclusion programs.

Ian Roberts, the superintendent, has been held in an Iowa jail since Friday. Immigration and Customs Enforcement officials have said that Dr. Roberts, who was born in Guyana and has long worked in school systems in the United States, had no legal status and had been ordered to leave the country last year.

“Out of concern for his 30,000 students, Dr. Roberts does not want to distract the board, educators and staff from focusing on educating D.M.P.S.’s students,” his lawyer, Alfredo Parrish, wrote in the letter, which he said he intended to send to the school board later on Tuesday.

In a news conference on Tuesday, Mr. Parrish did not directly address whether his client had ever had permission to work in the United States. Mr. Parrish said Dr. Roberts is seeking to have the order of deportation against him stayed, and is working on a motion to reopen his immigration case.

Mr. Parrish showed reporters a letter that he said had been sent to Dr. Roberts earlier this year by a Texas lawyer who had represented him in his immigration case. In that letter, the Texas lawyer wrote, “I am pleased to report that your case has reached a successful resolution.”

Jackeline Gonzalez, the Texas immigration lawyer who represented Dr. Roberts, said in an email that she was seeking her client’s permission to provide details about his case.

Over about two decades, Dr. Roberts had moved from state to state, building a national profile as a schools administrator. He wrote books, spoke at conferences and supported racial equity programs, sometimes drawing criticism from conservatives.

In Des Moines, Dr. Roberts, a former Olympic runner for Guyana, had quickly become a well-known figure. He dropped in frequently on classrooms, challenged students to foot races and seemed to rarely be photographed wearing anything but a well-tailored suit.

The rapid turn of events in Des Moines, a left-leaning city in a state led by Republicans, had many students and parents angry or unsure what to believe. ICE said Dr. Roberts had been in possession of a gun and a knife when he was confronted by agents on Friday morning while driving a vehicle provided by the school district. Federal officials said he fled from officers before being arrested.

On Tuesday, hundreds of Des Moines high school and middle school students walked out of class to protest Dr. Roberts’s detention and, in some cases, raise broader concerns about ICE and President Trump’s agenda.

At Roosevelt High School on the city’s west side, more than 300 students walked around a neighborhood block carrying signs and chanting “education over deportation.” Outside Central Academy near downtown, more than 150 students walked out of class and marched to the governor’s mansion.

Ian Schaffer, 18, a rally organizer and a high school senior, expressed concern about the circumstances of Dr. Roberts’s detention and described him as someone “who has put so much of his life into helping our educational systems in America.”

But the protest focused largely on broader concerns about immigration enforcement and what some students saw as an erosion of freedom of speech.

“The government hates people speaking out,” Mr. Schaffer told the crowd. “This administration thrives on people being silent.”

Dr. Roberts, who was placed on paid leave on Saturday and unpaid leave on Monday, had been given a noon Tuesday deadline by the school board to provide documents refuting ICE’s claims that he was in the United States illegally.

The Des Moines School Board is scheduled to meet on Tuesday night to consider Dr. Roberts’s job status. Phil Roeder, a spokesman for the district, said the resignation of an employee under contract requires board approval. He said on Tuesday afternoon that the district had just learned of the Justice Department’s investigation. “We are reviewing their letter and will respond to them accordingly,” he said.

The Justice Department’s investigation fits within the Trump administration’s broader priority of ending racially conscious education programs, including those that seek to hire a more diverse set of teachers and administrators.

“D.E.I. initiatives and race-based hiring preferences in our schools violate federal anti-discrimination laws and undermine educational priorities,” Harmeet K. Dhillon, who leads the Justice Department’s Civil Rights Division, said in a statement announcing the Des Moines investigation. “School districts must cease these unlawful programs and restore merit-based employment practices for the benefit of both students and employees.”

In 2021, before Dr. Roberts was hired, the Des Moines school system released its affirmative action program, which identified Black males as the student group with the lowest achievement, and in response, committed to recruiting more nonwhite educators.

For years, such efforts had bipartisan support. Policymakers generally agreed that students benefit from seeing diverse role models at school.

But race-conscious hiring has increasingly come under fire from a network of conservative advocacy groups with close ties to the Trump administration. One of those groups, Defending Education, published a February report critiquing Des Moines’s racial equity efforts.

Sarah Parshall Perry, vice president of Defending Education, questioned the Des Moines School Board’s vetting of Dr. Roberts in a statement after his arrest, saying that board members had been “more concerned with playing politics with race than with the qualifications of their leader or the safety of their students.”

School board leaders said Dr. Roberts claimed to be a U.S. citizen when he was hired and said outside firms were involved in reviewing his background.