The Mater has issued a statement saying it has reported all cases of Covid-19 positive results to the relevant authorities "on a daily basis".
The hospital was reacting to reports linking it to a large number of cases which were only reported to the Health Protection Surveillance Centre yesterday.
"At all times the Mater Hospital provided the information that the HSE required and met all legal requirements to report infectious diseases," the statement said.
"All of this information is correct and up to date.
"We are working with the HSE to understand why the provided data may not have been accurately captured.
"The Mater Hospital has also carried out comprehensive contact tracing on every single member of staff who tested positive for Covid-19 through our occupational health department in line with best practice.
"In excess of 300 staff at the Mater have tested positive for Covid-19 and a further 1,500 have self-isolated following contact tracing to protect patients, fellow staff and the public - despite the enormous impact this has had on our operations."
This morning, the Health Minister said the bulk reporting of Covid-19 cases by one hospital needs to be checked to see if it is a criminal matter.
Hospitals have a legal obligation to report cases of infectious diseases as soon as they are aware of them.
Simon Harris said it is "extremely disappointing" that this happened and he is awaiting a full report.
Last night, Chief Medical Officer, Dr Tony Holohan, said that there is an expectation and an obligation in the legislation for people to make those notifications.
“We want to encourage appropriate reporting and timely reporting and comprehensive reporting, a high standard of collection of all the key information in respect of all the cases and to have that reported to us in as timely a way as possible.”
He said he could not be certain the required contact tracing had been carried out for the cases who had tested positive in the hospital, but he expressed hope it would have been done.
“I would like to think the contact tracing necessary in the hospital environment by the occupational health teams might have been carried out but I don’t know that as a fact,” he said.
Paul Moynagh, Professor of Immunology at NUI Maynooth, says it would be very concerning if contact tracing hasn't been carried out.