Around 100 police officers sealed off the Twelve Tribes farm-based community in Deiningen, near Augsburg, Bavaria at around 6am on Thursday, and then moved in to take 28 children. They were removed in minivans and taken to foster families, under the custody of the authorities. Another 12 children were taken from a second location near Wörnitz
A police spokesman said there was no violence during the operation.
The dawn raids followed "new evidence pointing to significant and ongoing child abuse by the members", local officials were quoted as saying.
The Christian sect, which has bases in countries around the world, and says it has several thousand members, regards both Old and New Testaments as God's direct word.
They do not send their children to public schools, choosing to educate them within the community. Parents are taught that when children break rules, they are to "spank them with a small reed-like rod which only inflicts pain and not damage," they say on their website.
The Augsburger Allgemeine newspaper reported that the sect had often come to the attention of the public prosecutor which had investigated claims that five members had been involved in beating children. No charges resulted.
The Bavarian state withdrew its education license from the Twelve Tribes school at the complex at the end of July due to a lack of suitable teachers, leaving the parents of 20 school-age children obliged to send them to outside schools.
"The operation today did not have anything to do with topic of school attendance," a spokesman for the state education ministry told the paper.
US-founded Twelve Tribes said in an online statement: "We are an open and transparent community that does not tolerate any form of child abuse. Our children grow up in a loving environment and are educated in the spirit of charity."