Around 2.28 million sixth-graders and third-year junior high school students took the national achievement examination Wednesday in a region-by-region and school-by-school check of academic ability.
While all public schools participated, 52.2 percent of private schools did not, the education ministry said.
It was the first time in four years that all public schools were required to hold the exam, a policy expected to continue.
On Wednesday, some 1.15 million sixth-graders at 20,634 elementary schools and around 1.13 million students at 10,328 junior high schools took exams in Japanese and mathematics.
Next month, the ministry will ask about 50,000 parents how much they earn and how much they spend on children's education to study the link between income and academic performance.