There was new evidence of ongoing child abuse by members of the Twelve Tribes sect, officials told Germany's Spiegel Online website.
Witnesses of the dawn raids said there was no resistance from the group members, who denied the allegations, Augsburger Allgemeine reports.
The US-founded sect says it believes in spanking children if disobedient.
But it said a "small reed-like rod" was used intended only to inflict "pain and not damage" and was not abusive.
"Desiring to be good parents, we do not hit our children in anger, nor with our hand or fist," the group, which has communities in 10 countries around the world, says on its website about raising children.
"We know that some people consider this aspect of our life controversial, but we have seen from experience that discipline keeps a child from becoming mean-spirited and disrespectful of authority."