The HSE says it will suspend the practice of telling employers about the COVID-19 test results of workers before the staff themselves are informed.
It follows confirmation it had taken place in some circumstances.
Earlier today, it emerged that the Data Protection Commission is examining complaints about the issue.
Chief Medical Officer Dr Tony Holohan said any such cases would be a "breach of confidentiality, full stop".
HSE boss Paul Reid, meanwhile, told the COVID-19 committee they were aware of at least one case where it had happened.
In a statement this evening, the HSE said in most normal circumstances a staff member would be informed of their test results before an employer.
However, they note: "It is only in the most exceptional circumstances that HSE would consider informing an employer of an employee’s test result prior to informing the employee.
"This course of action would only be considered where it was considered essential for the public health good in all the circumstances.
This also would be a decision made by Public Health if it was considered in the best interest of the employee or a group of employees at the time, usually in the context of investigation of an outbreak and limiting onward transmission of infection."
Following the concerns raised today, the HSE says they will now suspend the practice.
Their statement explains: "In view of the concerns raised by some employees in relation to this issue, the HSE will reconsider the use of exceptions and has suspended the practice while we seek guidance from the Data Protection Commissioner."