The education ministry said the extra day off had given wealthier pupils an unfair advantage as they were being privately tutored out of school hours.
It will let schools re-establish Saturday classes. Where state schools fail to do that the government will pay for poorer pupils to attend crammer schools in the evenings and at weekends.
The switch was prompted by Japanese students falling lower in the international attainment league. It reverses a decision four years ago to bring in "relaxed education" aimed at creating more well-rounded citizens.
Saturday schools, then the norm were scrapped and teachers were told to stop setting the massive amounts of homework usually required even of the youngest students.
This led to an outcry from most parents who feared children would not get enough tuition to get through "exam hell" and into a good university. It has also created a boom for crammer schools, despite a declining birthrate.
Surveys suggest Japanese children typically study four to six hours per day outside school.