But there is better news in the study for British Prime Minister David Cameron. He is rated as the most trusted of EU country leaders. The majority of Germans also said they wanted to see Britain stay in the union.
The study was carried out by think-tank Open Europe Berlin and asked 1,010 respondents to rate their confidence of EU institutions. The European Commission and Parliament fared worst, with two-thirds expressing scepticism towards the bodies.
Half of respondents agreed with the statement that European politicians pursuing a policy of decentralization should be supported and two-thirds believed Germany should contribute less to the EU budget.
However a majority believed the EU should maintain its strong influence in the areas of fishing regulation, food safety and environmental protection.
Nora Hesse, deputy head of the Berlin branch of Open Europe, said the results marked the emergence of a distinction between the idea of Europe and the policies of the EU.
"German citizens remain pro-Europe on an emotional level. But they have begun to consider the EU as they would an ordinary government and are thus more inclined to consider Brussels just as - if not more - critically and sceptically than Berlin."
The study also found that the majority of Germans consider France their most important political and economic partner.
"This is partly down to tradition," Hesse told The Local. "Most people associate the idea of European integration with the relationship between France and Germany."
Despite the tendency to favour a scaling down of EU influence in many areas, a majority (57 percent) of Germans believe a British exit from the EU would be harmful to its image and credibility and that the next government should make an active effort to prevent it.
Among the EU member states, Germans expressed most confidence in British prime minister David Cameron rather than in French president Francois Hollande.
"This could have to do with personality," Hesse said. "But it's also likely to have something to do with Britain's emphasis on keeping Europe competitive."