At least 22 universities and research institutes have confirmed accepting more than €10 million in Pentagon research grants since 2000, the Süddeutsche Zeitung newspaper said on Monday.
Its research, conducted with broadcaster NDR, revealed that although there were some cases of US Defence Ministry money being used for basic research, other projects were clearly military.
It is this that critics say is impossible to square with academic ethics. "Research for war is not ethically responsible," said Reiner Braun from the Federation of Germany Scientists.
The University of Bremen takes funding from the Pentagon even though it has an explicit commitment to conduct research only for civilian purposes, the Süddeutsche said.
Yet the university said its research into satellite technology was "purely civilian basic research". The US funding is organized so that the Defence Ministry can pump money into non-military research projects.
Munich's Ludwig-Maximilian University (LMU) received more than €470,000 from the US Defence Ministry for research to improve military explosives, while the Fraunhofer Society, a nationwide network of research institutions, is working on bullet-proof glass and explosives.
Professor for inorganic chemistry at LMU Thomas Klapötke said he had no problem working with nearly half a million dollars of Pentagon money in his project to develop more environmentally-friendly explosives.
"If you believe in the Nato alliance, there is nothing wrong with kitting out your own people with good material," he said. He told the Süddeutsche that a large share of the funding for his research came from military sources.
The University of Marburg is researching navigation systems for drones and "steered munitions". Meanwhile, scientists at the University of Saarland received more than €130,000 from the US Army Research Laboratory for the mathematical research of language structure. The university said this was pure research, the results of which could have many uses.
Many scientists were constantly on the hunt for funding to boost their research budgets. But a spokeswoman for the LMU stressed that the US military cash made up significantly less than one percent of all outside funding.