Teachers and students will share the same toilets at all schools under the Office of the Basic Education Commission (Obec).
The change has drawn anger on a social media platform operated by the Education Ministry.
Obec announced that in future there will not be separate toilets at schools for teachers and students, in a message posted on the ministry's Facebook account.
Toilets will be separated only by gender, males and females.
The change was part of a plan for cleaner school toilets and was a policy of Education Minister Permpoon Chidchob.
The minister had previously angered people when he expressed admiration for the education system in North Korea and the strict discipline imposed on youngsters there.
Obec will start improving toilets firstly at its 9,700 small schools with no more than 80 students, and later at larger schools. However, the shared toilet policy will be introduced at all schools this semester, Obec said.
A survey of students showed they wanted cleaner toilets at schools, according to Obec. "Toilets for teachers are heaven. Toilets for students are hell," the ministry quoted one comment made during the survey.
One former Obec board chairman criticised the plan, saying that all toilets at schools, both for teachers and students, needed to be cleaner, but students should also have respect for their teachers. Thai culture could suffer if there was no boundary between teachers and students, he warned.
Comments posted following the ministry's announcement said students' toilets were dirty because the children made no effort to keep them clean or to help the school janitors, who were overworked.
