The Chief Secretary, Mr Rylah, said this today.
The files would be studied by officials of the Crown Law and Health Departments, who would report to him "in due course."
Mr Rylah said yesterday's police swoop, less than half an hour after scientology had been outlawed by the State Government, had cleaned out all the records at the Spring St. centre.
But police were continuing efforts to track down files elsewhere.
An examination would be made of the files to see how complete they were, and a list would be compiled.
Files and records submitted at the marathon 159-day scientology inquiry would remain in the Government's possession.
Mr Rylah would not say why the Government had not immediately burned the 400 personal files collected yesterday.
In his report to the State Government on scientology, Mr. K. V. Anderson, QC, said:
"There was no evidence that blackmail in the legal sense had been practised - but the basis for such criminal activity exists in the files of the organisation.
"The existence of these files containing the most intimate secrets and confessions of thousands of individuals is a constant threat to them and a matter of grave concern.
"This aspect is the more serious because copies of these reports are also held in England."