The first survey to rank German universities' research performance found that only a small number perform at top capacity compared with their international counterparts.
Humboldt University in Berlin, Ludwig Maximilian University in Munich and the University of Freiburg came out top in the study, which began in 1997.
"We have a whole stack of faculties performing well in research fields," said Detlef Müller-Böling, director of the Centre for University Development (CHE) in Gutersloh. "Yet real research universities, such as you have overseas, are hard to find in this country."
The faculties assessed included engineering, economics, social sciences, humanities, management and business studies, English, German, history, psychology and behavioural sciences.
The CHE assessed the number of registered patents, publications, completed doctorates and sources of extra funding at the universities.
Additional funding was possibly the most important criterion, categorised by success in obtaining funding from sources outside the budget granted by each state. The calculations exclude grants and scholarships from foundations such as the Volkswagen, Humboldt and the German Research Foundation but include funding won by individual professors or departments from industry and commercial sponsors.
Nationally, half of additional funding goes to only about 30 per cent of the universities.
The other component of the survey was opinion among German professors on which university had the best reputation for each discipline.
"The main aim was to make the performance of German universities transparent on a national level and to highlight those faculties that are outstanding," a CHE spokesman said.
The outcome shows that a considerable number of German universities contribute no significant research to their fields, publish little and do not cultivate scholars for the next generation, judged by the lack of dissertations in their departments.
But not even the three top performers won in every category: Humboldt and Ludwig Maximilian succeeded in seven of the nine faculties surveyed, while Freiburg excelled in six of the eight fields.
CHE based its study on data collected by Stern magazine, which has been publishing university rankings in Germany for the past five years.
Stern 's ranking covers 25 subjects offered in higher education and is concerned with conditions for students as well as staff performance.
The CHE said it would produce another research ranking of German institutions next year, concentrating on information technology, mathematics and science.