Pupils' performance in different types of schools were compared by researchers working on behalf of the Organisation for Economic Co-operation and Development (OECD) at Germany's Max Planck Institute for Educational Research in Berlin. They also took a close look at school marking systems.
The Pisa III results show that standards are wildly uneven both at state level and within schools themselves, with each school applying its own criteria for testing and marking - the downside of Germany's federal system where the 16 states are responsible for education.
Experts comparing grammar schools in six states cited absurd examples where average marks for the same test ranged from A to C.
They discovered that many pupils at ordinary schools performed better in maths than their grammar-school counterparts. Bright children were stuck in low-ranking schools, while schools with high academic pretensions had many poor performers. Overall, many children had been assigned to the wrong schools.
Researchers at the institute suggest phasing out secondary selection. They also recommend laying down national guidelines to combat the divergences in school marks.
The Kultusministerkonferenz (KMK), a key forum which represents the country's education ministers, now aims to introduce national standards and testing for the first time next year.
However, KMK president Karin Wolff, who is also education minister for Hesse, has reaffirmed her commitment to an academically selective school system.
One solution to regional disparities could be the introduction of all-day school. At present, the school day ends at 2pm. But Karin Wolff is not convinced. "All-day schools don't necessarily mean better standards," she told The TES. "A successful education system is about more than just a longer school day."
The KMK intends to start by bridging the notorious gap between German kindergartens and primary schools by encouraging standard early-learning concepts. Children could then start school sooner, between the ages of five and six.
Germany's primaries in turn face problems of their own. Pisa III revealed that a large number of ethnic-minority children with poor German can dramatically lower a school's academic performance.