"Cost-effective learning" compared 1,035 state schools with 54 independent schools on the basis of teachers' grades and test results, the number of students passing exams and the number going on to upper-secondary school.
It concluded that independent schools are more cost-effective and claimed that the high percentage of unqualified teachers - 49 per cent in the independent sector and 21 per cent in state schools - had no detrimental effect on the quality of teaching.
Sweden's minister for schools, Ibrahim Baylan, attacked the report, saying it was inaccurate and misleading to draw conclusions from such crude data.
In response, the National Agency took the unprecedented step of withdrawing the report, claiming it contained a number of unspecified errors.
The opposition was outraged. The Moderate party's education spokesman, Sten Tolgfors, said: "Baylan shouldn't try to influence an independent state authority."
The findings could influence the education debate in Britain, where Conservative leader Michael Howard said last June that Sweden achieved much better results than Britain because of its huge increase in non-state-run schools, giving parents the right to choose.
Sweden's national agency director Per Thullberg did not comment on the Government's criticism but confirmed that the report would "now not be widely distributed because it is open to misinterpretation".
It remains part of the agency's investigation into the connection between resources and effectiveness in schools.
Baylan's attack may be a veiled attempt by the government to reaffirm the credibility of state schools. It follows prime minister Goran Persson's suggestion that Sweden's relatively poor performance in the last round of the Programme for International Student Assessment tests might be a reflection of the number of unqualified teachers employed by schools.
One of the authors of the report, Jesper Antelius, maintains that independent schools are more cost-effective and efficient than state schools. This is primarily because they are successful in attracting motivated students from well-educated homes," he told Swedish newspaper SvD.
Antelius also believes: "Competition from the independent sector makes state schools use their resources more effectively. They also tend to try out new and more effective teaching methods."