"We ask for the cooperation of relevant ministries and agencies so that pupils and students will stay at home in principle and not go outside unless it is necessary," Hagiuda said.
The education minister said the decision was made by the government because "experts have been saying schools have a high risk of group infection."
Hagiuda's remarks were made as the education ministry had officially shut down Japan's elementary, junior and high schools from March 2.
The timing of the nationwide school closures comes a few weeks ahead of the schools' spring break scheduled for late March.
The announcement, however, has been met with some uncertainty from teachers, students and parents who have not been prepared for the unscheduled break.
Japanese Prime Minister Shinzo Abe on Thursday announced the plan to close all the schools at a government task force meeting on combating the coronavirus.