The ministry announced on Friday that in-person classes would be suspended in the affected schools.
Ten students and a faculty member had tested positive on Thursday from schools in Seoul, Gyeonggi, and South Chungcheong Province, spurring the decision to close schools.
On Friday, Korea's Disease Control Prevention Agency (KDCA) announced 145 new coronavirus cases. South Korea has reported more than 100 new daily cases for the past three days.
The country has recorded a total number of 27,195 confirmed cases and 476 deaths since the pandemic began, according to KDCA.