The education ministry conducted the tests in April, covering about 740,000 or 30 percent of all 6th grade elementary school pupils and 3rd-year junior high students.
Basic knowledge and application skills were tested in two subjects -- Japanese language and mathematics.
The results released on Friday show that in the basic knowledge tests, 83.5 percent of the 6th graders gave correct answers in Japanese language and 74.4 percent in mathematics.
The figures for the junior high students were 76.1 percent in language and 66.1 percent in maths.
In applications skills, however, 78 percent of 6th graders gave correct answers in Japanese language, and 49.6 percent in mathematics. Junior high students answering correctly totaled 66.5 percent and 45.2 percent respectively.
The education ministry says Japanese children are not sufficiently developing skills that enable them to express their thoughts in writing based on given information, or to think about daily occurrences in a logical way.
In geographical terms, students in Akita Prefecture, northeastern Japan, scored best.
The ministry says their high scores can be attributed to routine study hours at home.
A lifestyle survey conducted at the same time found that 79.6 percent of elementary school pupils in Akita study for more than one hour even on holidays. The figure is more than 25 percentage points higher than the national average of 54.5 percent.