The U.S. Department of Education on Thursday told employees that it would lift its monthlong freeze on investigating discrimination complaints at schools and colleges across the country — but only to allow disability investigations to proceed.

That means that thousands of outstanding complaints filed with the department’s Office for Civil Rights related to race and gender discrimination — most of which are submitted by students and families — will continue to sit idle. That includes cases alleging unfair discipline or race-based harassment, for example.

“I am lifting the pause on the processing of complaints alleging discrimination on the basis of disability. Effective immediately, please process complaints that allege only disability-based discrimination,” Craig Trainor, the office’s acting director, wrote in an internal memo obtained by ProPublica. It was sent to employees in the enforcement arm of the office, most of whom are attorneys.

A spokesperson for the department did not immediately respond to a request for comment.

ProPublica reported last week that the Department of Education had halted ongoing civil rights investigations, an unusual move even during a presidential transition. Department employees said they had been told not to communicate with students, families and schools involved in cases that were launched in previous administrations, describing the edict as a “gag order” and saying they had “been essentially muzzled.”

The office has opened only a handful of new cases since the inauguration of President Donald Trump, and nearly all of them reflect his priorities. The investigations target a school district’s gender-neutral bathroom and institutions that have allowed transgender athletes to participate in women’s sports. Other prioritized investigations involve allegations of discrimination against white students or of anti-semitism.

As of last week, the OCR had opened about 20 new investigations in all, a low number compared with similar periods in prior years. More than 250 new cases were opened in the same time period last year, for example.

The OCR has had a backlog of cases for years — there were about 12,000 pending investigations when Trump took office. Some had been open for more than a decade, which civil rights advocates said failed to bring relief to students when they needed it.

About half of the pending investigations are related to students with disabilities who feel they’ve been mistreated or unfairly denied help at school, according to a ProPublica analysis of department data.

Investigators were pursuing about 3,200 active complaints of racial discrimination, including unfair discipline and racial harassment. An additional roughly 1,000 complaints were specific to sexual harassment or sexual violence, the analysis found. The remainder concern a range of discrimination claims.

Ignoring or attacking disability rights “would be politically unpopular,” said Harold Jordan of the American Civil Liberties Union, who works on education equity issues across the country. “They don’t want to be seen as shutting down all the disability claims,” he said.

But complaints typically investigated by the OCR, many related to discrimination against students of color, do not align with Trump’s priorities on racial bias, which so far have related to prejudice against white students.

“They will pick up race cases once people file, essentially, reverse discrimination complaints,” Jordan said.

The OCR, in fact, decided this month that it would investigate a complaint filed in August by the Equal Protection Project, a conservative nonprofit, that alleges the Ithaca City School District in New York excluded white students by hosting an event called the Students of Color Summit. The Biden administration had not acted on the complaint, but new Education Department leaders decided within days that the agency would proceed with an investigation.

Thursday’s memo also included a “revised” case manual, which details how the office will investigate and resolve complaints that allege violations of civil rights law. During the previous administration, investigators had the authority to open “systemic” inquiries when there was evidence of widespread civil rights issues or multiple complaints of the same type of discrimination at a school district or college. That ability to launch wider investigations appears to have been stripped under Trump; there is no mention of systemic investigations in the new manual.

The manual also no longer includes gender-neutral references; people alleging violations of “their” rights have been replaced by “his or her” in Trump’s updated version. That aligns with his recent anti-transgender policies and his view that there are only two genders.

The shifts at the OCR come as Trump has called the Education Department a “con job” and is expected to issue an executive order that it be dismantled. Last week, Trainor told schools and colleges that they have two weeks to eliminate race as a factor in admissions, financial aid, hiring and training or risk losing federal funding.

“Under any banner, discrimination on the basis of race, color, or national origin is, has been, and will continue to be illegal,” Trainor wrote.

During the past two weeks, the Trump administration has terminated contracts totaling hundreds of millions of dollars that mostly focused on education research and data on learning and the country’s schools. The cuts were made at the behest of Elon Musk’s cost-cutting crew, known as the Department of Government Efficiency, which said it also ended dozens of training grants for educators that it deemed wasteful.

But recent contract terminations touted by Musk’s team as ridding the department of “waste” and ending “diversity” programs also abruptly ended services for some students with disabilities.