Only six of the eight commissioners voted to express concern about the Trump administration's handling of civil rights, while two voted against it, according to a spokesman for the commission.
Others, who believe that students must use bathrooms according to their biological sex rather than their gender identity, have welcomed the Trump administration's change of course on complaints involving transgender students.
The investigation will also look into the departments of Labor, Housing and Urban Development, Health and Human Services, Environmental Protection Agency and the Legal Services Corporation - which are all expected to slash budget and personnel that monitor civil rights. Specifically, the instructions say that investigators should not reject gender harassment allegations in a complaint, even if they have dismissed allegations involving "denial of access to restrooms based on gender identity".
In the administration's budget request for the fiscal year that begins in October, the Education Department has proposed cutting more than 40 staff positions from the office for civil rights, which would require the office to "make hard choices, including cutting back on initiating proactive investigations", the department wrote.
"If a child cannot use the right bathroom at school, they simply cannot go to school, they cannot be a student", said Mara Keisling, executive director of the National Center for Transgender Equality.
While working under Obama, Lhamon helped write guidance explaining to schools that Title IX, a federal law that prohibits sex discrimination, protects students' right to use bathrooms matching their gender identity. Education officials said they wanted to emphasize that transgender students may still have valid discrimination complaints despite the rescission of that guidance.
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Keisling said her organization is still trying to determine what this memo portends in a legal framework, and until then said she "would not be surprised if this turns out for the worst".
The Leadership Conference on Civil and Human Rights has condemned the announcement by the Department of Homeland Security (DHS) that it was rescinding the memorandum that created the Deferred Action for Parents of Americans and Lawful Permanent Residents (DAPA) program. "Along with changing programmatic priorities, these proposed cuts would result in a unsafe reduction of civil rights enforcement across the country, leaving communities of color, LGBT people, older people, people with disabilities, and other marginalized groups exposed to greater risk of discrimination".
Secretary of Education Betsy DeVos will be downsizing the number of investigations it conducts into possible civil rights violations throughout the public school system, the New York Times reported on Saturday. Jackson also recently defended new policies on the rights of trans students after one employee told the Huffington Post "officials should investigate issues of discrimination just as they would have before the Obama-era rules were implemented".
Elizabeth Hill, a spokeswoman for the Education Department, said the change in approach is meant to confront the agency's infamous complaint backlog and ensure that investigations are resolved more quickly. But critics of the Trump administration considered the narrowing of some investigations as another example of an effort to narrow civil rights enforcement.
Some enforcement officers at the Office for Civil Rights, who have long complained about being overburdened, embraced the new flexibility.
Education Department cautioned against construing the closure of the cases as any statement about the Trump administration's view of or approach to transgender students' rights. Patty Murray (D-Wash.) said in a statement.