The Data Protection Commissioner has begun a statutory inquiry into the handling of sensitive personal information by the Department of Health.
The office has acted on its own initiative to set up the inquiry having already submitted questions to the department following a report by RTÉ Investigates last week.
In the programme, RTÉ Investigates detailed how the Department of Health has been secretly using information from private doctor consultations to build and maintain dossiers on children with autism who were involved in legal actions against the State.
A statement from DPC said the issue arose in relation to information on children diagnosed with autism who had been involved in legal actions against the State.
"The inquiry will examine whether or not the Department of Health has discharged its obligations in connection with the data processing concerned and it will determine whether or not any provisions of the Data Protection Acts and/or the GDPR have been contravened by the Department of Health in that context," it said.
Authorised officers of the DPC have been appointed to conduct the investigation.
Under the Data Protection Act, these authorised officers have the power to enter premises, search for, secure and inspect any documents if the investigation requires it.
The Secretary General of the Department of Health, Robert Watt, wrote an open letter following the report that it had not acted unlawfully.
"I would like to reassure all parents, families and interested parties that the department has never unlawfully held sensitive medical and educational information of children involved in dormant court cases," he said.
Inclusion Ireland, the national association for people with an intellectual disability, said the programme findings have "seriously damaged faith in the system among people with disabilities and their families".
Interim CEO of Inclusion Ireland Lorraine Dempsey said: "We know that 50 children are affected by this investigation, but every family who has interacted with State agencies or advocated on behalf of a child with a disability is now wondering if their information has been retained, or collated. Faith in the system has been seriously damaged by the revelations.
"We're calling for a full investigation into this practice to establish how widespread it is, how many people are affected, and if people's rights to privacy have been breached."
