The statistics, compiled into a report by the Lärarnas tidning trade journal, show that there is some significant discrepancy between final grades awarded to girls and boys in relation to the respective performance of the groups in national tests.
Students in class nine (15/16-years-old) complete national tests in six key subjects - Swedish, English, Mathematics, Biology, Chemistry and Physics. Generally the results in these tests were shown to be lower than final marks awarded to students, the journal concluded, with girls benefiting the most from the discrepancy.
According to the report, the statistics reveal that in English, for example, there were 50 percent more girls than boys who received higher final marks than their performance in the national tests warranted.
In Swedish the difference was observed to be 40 percent.
"But this is a rather curious way to read our statistics," Roger Persson at the Education Agency told The Local on Thursday.
"The figures, in English for example, do in fact show that 7 percent of boys received a higher final mark than in the national tests, and that 11 percent of girls did so - a difference of around 50 percent. But they also show that 8 percent of boys received a lower final grade, as did 5 percent of the girls," Persson explained, arguing that sweeping conclusions can't be made as to the underlying reasons.
Education minister Jan Björklund on Thursday also questioned whether the statistics show that boys are systematically treated unfairly in Swedish schools' marking system.
"The final marks should not be a carbon-copy of the results in the national tests, they should also weigh in the student's work in lessons. It could easily be that girls simply perform better in lessons," Björklund said, according to news agency TT, on Thursday.
The National Agency for Education describes the national exams as an "assessment support" for teachers, explaining that the tests are designed to develop grading consistency across the country while allowing scope for a broader assessment.
Björklund argued that changes in teaching and developmental factors could easily explain the apparent differences.
"The statistics illustrate an educational trend in which students are expected to take a greater responsibility. We know that girls generally mature earlier than boys and thus it may be that they have greater ability to take responsibility for different tasks in class."
Persson told The Local that the agency is unable to conclude why there is a general trend showing that girls received higher final marks in schools than boys and argued that further research is needed in the area.
"It can't be ruled out that other factors, other than knowledge, are considered by teachers, but the national tests do not measure all the curriculum's goals."
Björklund also remained open to the possibility that boys are unfairly missing out on higher marks and stated that it is the job of the Schools Inspectorate (Skolinspektionen) to determine if any discrimination is occurring.
"It is an important part of the Schools Inspectorate work to monitor this aspect, and if there is a problem, it should be corrected,” he said.
In response to the report, the Swedish Teachers' Union (Lärarförbundet) has called for more support for its members to enable them to increase cooperation and objectivity when its comes to awarding final marks.
"The teaching profession is currently too much of a solo job. Teachers need to both receive and take the time to discuss grades and evaluation with colleagues," said union president Eva-Lis Sirén on Thursday.