A supplementary examination of a 2003 international study has revealed significant differences between the cantons' education systems.
French-speaking pupils from Fribourg have done best, but Swiss teachers have sharply criticised the rankings.
The Programme for International Student Assessment (Pisa) - run by the Paris-based Organization for Economic Cooperation and Development - measures the skills of 15-year-olds in four categories: maths, reading, science and problem-solving.
Twelve cantons – as well as the neighbouring principality of Liechtenstein – took part in the comparison. To a large extent, it confirmed the findings of the most recent Pisa study in 2003, which was published last December.
The year-nine students from Fribourg topped the list in maths, science and problem solving.
In maths – a main focus of Pisa 2003 – the Fribourg pupils saw off competition from the cantons St Gallen, Thurgau and Valais; in science from Valais and Liechtenstein; and in problem-solving from Thurgau and Valais.
The Federal Statistics Office said on Monday that students from the cantons of St Gallen, Thurgau and Valais were also above average.
Only when it came to reading were the students from Fribourg not the best – their colleagues in Liechtenstein and Thurgau were the most literate.
At the other end of the league table were students from cantons Bern, Geneva, Ticino and Vaud.
Maths is at a high level almost everywhere, but reading skills are weak in every canton.
The use of computers is also below average. Although most teenagers use a computer at home several times a week, only one student in three uses a computer regularly at school, despite most establishments being equipped with them.
The Statistics Office said that compared with most other countries surveyed in the Pisa study this was a small proportion of users.
The results showed once again that students’ social and cultural backgrounds have a critical influence on their performances. Young people from social backgrounds where education is not a priority tend to do worse.
But many educators have reacted angrily to the study, saying it ignores important explanations for the differences in the cantons’ performances.
Hans Ulrich Stöckling, president of the conference of cantonal education ministers, said that the school system of individual cantons didn’t have any influence on how well year-nine students did in the tests.
In Ticino, where pupils scored the lowest points for maths, the authorities responded by saying that it was the canton "that assured the best equality between pupils" and that it had the smallest gap between more gifted and less able children.
The Pisa results from 2000 revealed that a fifth of Swiss pupils could at best read a simple text by the end of their studies, igniting a heated debate across the country.
A real reform of the system will not be possible before the completion of the third Pisa study in 2007, when unified standards should be introduced nationwide.
swissinfo with agencies
In the 2003 survey Switzerland came seventh in maths, 11th in reading, ninth in science and eighth in problem-solving.
Cantons Fribourg, St Gallen Thurgau and Valais were all above average.
Bern, Geneva, Ticino and Vaud were at the bottom of the rankings.
Every three years, the Programme for International Student Assessment (Pisa) measures 15-year-olds in four categories; maths, reading, science and problem-solving.
Internationally standardised testing methods are used.