Mr Hague claimed 30,000 children had received the leaflets from the group.
He said the church was against the use of medicines used to treat mental illness and psychiatry and targeted vulnerable members in the community.
"It is evil to try to dissuade people with mental illness to avoid proper health professional services that they need."
"I don't object to churches providing social services, provided the church is transparent and that the service is not a front for recruiting into the church, but the Church of Scientology fails of both of those fronts."
Mr Hague said that among the groups acting as a front for the Church of Scientology were Drug-Free World, Drug-Free Ambassadors, Commission for Human Rights, Rehabilitate New Zealand and World Literacy Crusade.
He called for the Minister of Internal Affairs to follow through with an investigation promised by the department in February.
Church of Scientology secretary Mark Ferris confirmed Drug-Free Ambassadors and Drug-free Aotearoa were registered charities and had received a $6500 community grant to fund fliers promoting a drug-free life.
Mr Ferris said the groups listed in Parliament by Mr Hague were well-known affiliates of the church.
He said the leaflets were distributed widely and had not targeted children and did not address psychiatric drugs.
He said Mr Hague's comments were not accurate.
"They are stupid, because we are doing something in terms of drug education that no other group is," he said.
Mr Ferris said the church was against the over-use of medication in psychiatry but not against medication overall.
"They are saying that a drug-free life is better than taking drugs," he said.
"We use medical doctors like anyone else. In fact, we have members of in the church who are doctors," he said.