Some 1,596 other schools reported less than 10 new students in 2013.
Most of the schools without newcomers are in rural areas, the data show.
Officials attributed the declining number of students to the country's chronically low birthrate.
"More than 50 percent of the primary schools in Gangwon and South Jeolla Provinces had less than 10 newcomers this year, reflecting their aging population in the remote regions and the subsequent lower birthrate than urban areas," an official told the Yonhap News Agency.
There were 2.95 million primary school students in 2012, a 5.8 percent decrease from a year earlier.
In 1980, there were 5.65 million primary students.