The investigation affected five American states.
According to the Ministry, such bans discriminate against students with disabilities.
The ministry sent letters to South Carolina, Tennessee, Utah, Oklahoma, and Iowa officials, which banned local school districts from introducing a mandatory mask regime.
The letters claimed that the states might be preventing school districts from meeting the needs of students with disabilities who are at increased risk of serious illnesses if they become infected with the coronavirus.
Earlier this month, U.S. President Joe Biden said that the Department of Education would use its powers to block attempts by states to prevent school districts that want to introduce mandatory wearing of masks.
In some states, Republican governors who are critical of the Democratic president believe that wearing masks should be a personal choice of parents and families.