The sect, founded by a Tennessee high school teacher in the 1970s, today has about 2,000 to 3,000 members worldwide, according to its website.
They have previously had problems in Germany for violating laws on homeschooling their children.
The sect's practices have run afoul of the law in the U.S. as well, including in 2000 in Connecticut where a couple belonging to the group pleaded guilty to third-degree assault and cruelty for disciplining their children with a 30-inch (76-centimeter) fiberglass rod.
In 1984, authorities raided the group in Vermont and removed 112 children on abuse allegations. A judge later ruled the raid illegal and returned the children to their parents.
The raids in Germany came after an undercover reporter for RTL television passed on evidence he had accumulated over months of work, the station reported.
Engelsberger said he could not comment on where the tip came from, but said initially an area family court had ordered the children removed after receiving evidence, then his office began a legal probe after the sticks and other evidence were found during the raids.