The events began when police raided the sect’s farm in Oratorio, south-east of Guatemala City, on Friday, taking the children into care.
Prosecutors said there were suspicions of “forced pregnancy, mistreatment of minors and rape”.
But two days later, about 100 of the children’s relatives – all members of the sect – gathered outside the centre where they were being held to call for their return.
Some sect members then forced open the gate and tried to abduct the children and adolescents sheltered there, the Attorney General’s Office said.
But the children were intercepted by the authorities and put into a white minibus, local media reported.
With police help, the centre “managed to locate and protect everyone again”, the Attorney General’s Office added.
Officials had previously tried to check on the children’s wellbeing, but were prevented from entering the farm by sect members.
Authorities estimate that the community is made up of about 50 families residing in Guatemala, the US, Canada and other countries.
The Jewish Community of Guatemala has issued a statement disowning the sect, describing it as foreign to its own organisation.
It expressed support for the Guatemalan authorities in carrying out necessary investigations “to protect the lives and integrity of minors and other vulnerable groups that may be at risk”.