Extracts from the study seen by Die Welt show that around half of the menus checked didn't have enough vegetables in them.
"As always, meat shows up too often in the meals," the study authors from the Hamburg School of Applied Research write.
Many pupils are unhappy with the food on offer. Just 53 percent thought it was "good" or "very good" in primary school, while numbers were even lower for older pupils.
They may have good reason, as just 16 percent of primary schools and 27 percent of secondary schools had two or more menus at lunch.
The Ministry also finds that lunch breaks are too short, with just 39 percent of schools having one that lasts 45 minutes or more as recommended by the German Nutrition Society (DGE).