Announced on Monday, the move comes as multiple states have challenged masking in schools. The department's Office of Civil Rights (OCR) is focusing on five states – Iowa, Oklahoma, South Carolina, Tennessee and Utah.
"The Department has heard from parents from across the country – particularly parents of students with disabilities and with underlying medical conditions – about how state bans on universal indoor masking are putting their children at risk and preventing them from accessing in-person learning equally," U.S. Secretary of Education Miguel Cardona said in a press release.
"It’s simply unacceptable that state leaders are putting politics over the health and education of the students they took an oath to serve. The Department will fight to protect every student’s right to access in-person learning safely and the rights of local educators to put in place policies that allow all students to return to the classroom full-time in-person safely this fall."
OCR will be investigating whether the states comply with Section 504 of the Rehabilitation Act of 1973 and Title II of the Americans with Disabilities Act of 1990. Both address discrimination based on disabilities.
The move will likely provoke backlash from conservatives who believe coronavirus restrictions have gone too far and could impact children's emotional health.
Fox News previously reported on an Oklahoma district school board member who apologized after suggesting that students could commit "murder" by not wearing masks. The state had prevented local districts from imposing mask mandates under certain circumstances.
"Until every American citizen is safely out of Afghanistan, President Biden shouldn’t spend a single second harassing states like Oklahoma for protecting parents’ rights to make health decisions for their kids," said Carly Atchison, communications director for Gov. Kevin Stitt.
"Forcing schoolchildren to mask all day in school flies in the face of science, especially given children’s low risk of severe illness and death and their low risk of transmission," Attorney General Eric Schmitt said in a statement. "Additionally, forcing schoolchildren to mask all day could hinder critical development by eliminating facial cues and expressions."
Fox News' Jessica Chasmar contributed reporting.