The Biden administration will use a federal civil rights office to deter states from banning universal masking in classrooms.

The nation’s most vulnerable students, namely students with disabilities, low-income students and students of color, have suffered the deepest setbacks when districts pivoted to remote learning, and their disproportionate disengagement has long drawn concern from education leaders and civil rights watchdogs.

Under Section 504 of the Rehabilitation Act of 1973, students are entitled to a free, appropriate public education, known as FAPE, and Title VI of the Civil Rights Act of 1964 prohibits discrimination based on race, color and national origin.

The department could initiate its own investigations into districts, if state policies and actions rise to potential violations of students’ civil rights. It could also review complaints from parents and advocates who make the case that prohibiting masks mandates is, in effect, a civil rights violation because it could deny a student their right to an education by putting them in harm’s way in school. Such investigations could result in resolution agreements, as many investigations by the office often do, and in the most extreme cases result in revocation of federal funding.

Dr. Cardona said conversations with parents of children with autism, respiratory illness or weak immune systems, “who rely on school for socialization and the important building blocks of learning,” had contributed to his sense of urgency.

“I’ve heard those parents, saying ‘Miguel, because of these policies, my child cannot access their school, I would be putting them in harm’s way,’” Dr. Cardona said. “And to me, that goes against a free appropriate public education. That goes against of the fundamental beliefs of educators across the country to protect their students and provide a well rounded education.”

The administration will also send letters to six states — Arizona, Iowa, Oklahoma, South Carolina, Tennessee and Utah — admonishing governors’ efforts to ban universal masking in schools.

Last week, Dr. Cardona sent similar letters to the governors of Texas and Florida, reminding them that districts had both the funding and the discretion to implement safety measures that the C.D.C. recommended for schools. The secretary also made clear that he supported district leaders who defied the governors’ orders.