The global rankings of the world's best universities show just 10 from Germany in the top 200 – down from 11 last year – and none in the top 50.
The Ludwig Maximilians University (LMU) in Munich was in 55th place – dropping from 48th last year.
Elizabeth Gibney from the Times Higher Education rankings told The Local the fall was down to the LMU dropping in two measurements used in the rankings.
In research and teaching it fell, but held up in its citation score and international outlook. She said: “There have been some falls across Europe that are concerning but overall the picture within Germany is still healthy.”
Although it has fewer universities in the top 200 this year, many have risen up the list with the Free University in Berlin showing the biggest leap.
Phil Baty, the editor of Times Higher Education Rankings, said: “Germany has not suffered as badly as many European countries as a result of the financial crisis and has robustly supported its top institutions.”
The University of Göttingen rose seven places to 63rd. Ruprecht Karl University of Heidelberg was also up from 78th to 68th, while the fourth highest German university was the Free University of Berlin up 40 places to 86th.
The other German universities to make the list were the Technical University of Munich (87th), Humboldt University of Berlin (94th), RWTH Aachen University (129), University of Freiburg (152), Karlsruhe Institute of Technology (154) and the University of Bonn (181). All rose in the rankings apart from the Freiburg, Bonn and Karlsruhe universities which were down slightly.
The California Institute of Technology retained its place at the top of the rankings for the third consecutive year, with Harvard University regaining second place (up from fourth), a position shared with the UK's University of Oxford. Stanford University slipped from joint second to fourth.
Europe generally fared badly this year. While the UK's number one, Oxford, held on to second place in the table, almost across the board the continent's top institutions lost ground.
Scandinavia was an exception to the trend, with its top institutions strengthening their positions.
The UK remains Europe's strongest representative, with 31 universities in the top 200. The Netherlands has 12 players, followed by Germany with 10, France with eight, Switzerland with seven and Belgium with five.
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