The announcement affects 1,845 schools across the nation, the first time since May that more than 1,000 schools will be closed, said the ministry.
A total of 283 students and 79 faculty members have tested positive for novel coronavirus since May 20 when South Korea began a phased return of pupils to the classroom, according to the ministry.
Countries around the world are currently grappling with how to keep children learning during the pandemic.
The world is facing a "generational catastrophe" because of school closures during the coronavirus pandemic, UN Secretary-General Antonio Guterres warned at the beginning of August.
"Getting students back into schools and learning institutions as safely as possible must be a top priority," once local transmission of Covid-19 is under control, Guterres added.