Just under a third of the country's 48,000 different animal species and 24,000 plant and fungi species are seriously threatened or are affected by a considerable decline in numbers.
These are the findings of a government study presented by Environment Minister Barbara Hendricks on Wednesday.
Only 25 percent of species populations were classified by the study's authors as being in a "good" state. Meanwhile, 29 percent were in a "bad" condition, especially butterflies, amphibians and migratory fish.
"If we want to keep our endangered animals and plants in Germany, we need to change course in several areas," said Hendricks in a statement.
Energy policy, agriculture and flood defences were key areas where strategic changes were necessary to help stop populations declining further, she said.
The study said the main causes of population decline were intensive agriculture and widespread use of fertilizers, as well as the loss of natural habitats to farming.
The minister said encouragement could be taken from improvement in some areas, with conservationists succeeding in bringing some species such as wild cats or sea eagles back from the brink.
"Here we can see that successes are possible in conservation," said Hendricks. "But in other areas nature is doing alarmingly badly.
"Butterflies and bees, for example, are suffering from the turning of flower-rich meadows into maize fields," she said.
The minister also called to an end to the expansions of biomass plantations.
"Today energy plants are growing on more than 17 percent of German fields - that is enough," she said.
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"Habitats used for agriculture are generally in a poor state from a conservation point of view," said Beate Jessel, head of the Federal Office for Nature Conservation (BfN) in the joint press statement, pointing to the loss of river meadows as a further cause of problems.
"River meadows do not only protect humans from flooding, they are also of vital importance to the survival of many species," she warned.