It comes as the Minister for Health called on bosses at the maternity hospital to explain why an RTÉ camera crew was allowed to film a programme while partners of pregnant women faced restrictions.
The latest series of The Rotunda, which documents the stories of expectant parents, started this week.
A spokesperson said: “The Rotunda very much regrets any upset or anxiety that the broadcast of this important documentary has caused, as none was ever intentioned.
“The Rotunda will continue to support and care for its patients and staff to the best of its ability, throughout both good times and challenging conditions.
“We will continue, in good faith, to always do our best for our patients and our families.”
However, the spokesperson also defended the decision to record the series.
They said: “Management at the Rotunda consider the series to be an important platform that enables patients to share their experiences, both good news stories and those that are heartbreaking.
“The Rotunda believes that it is important to hear these challenges and stories, and to acknowledge the experiences of patients and staff during the difficult time created by the Covid-19 pandemic.”
They also noted “the strong positive reaction (including from very senior politicians) to the RTÉ Investigates: Inside Ireland’s Covid Battle documentary series which was broadcast in July 2020.”
“That documentary was filmed at the height of the pandemic inside St James’ Hospital Intensive Care Unit, when even more restrictive conditions than have ever applied at the Rotunda were in place” the statement said.
“The Rotunda management team were reassured to note that some of the same production staff involved in that much-lauded documentary were involved in series three of The Rotunda.”
Both RTÉ and the Rotunda have faced widespread criticism after a film crew was permitted on site when partners of expectant mothers were forced to wait outside maternity hospitals because of Covid restrictions.
Earlier on Friday, Stephen Donnelly said the Master of the Rotunda should make a statement on its decision to go ahead with filming.
“Access to maternity services for partners has been a very, very important issue this year,” he said.
“There’s been an awful lot of very difficult cases. For me what has been particularly distressing is cases where there have been emergencies and partners haven’t been able to get in.”
Fianna Fáil senator Lisa Chambers said it was “wrong” to allow filming to take place.
“I was disgusted to see that programme air when mums were left alone, dads were left to wait in the carpark,” Ms Chambers said.
“It is wrong, Rotunda should answer questions on it, I think RTÉ should have known better than to do it.
A new series of ‘The Rotunda’ begins this evening on RTE 2.
In the first episode, Michelle and Clive return to The Rotunda, three years after the birth of their first child Zach. Zach was born prematurely and sadly passed away. pic.twitter.com/xG2U42tneP
— The Rotunda Hospital (@RotundaHospital) September 8, 2021
“It is just compounding the hurt that many parents across the country feel when they remember the experience that they have been through.”
Taoiseach Micheál Martin said there should be “consistency” when making clinical decisions.
“Fathers and partners shouldn’t be facing restrictions and I’ve have been consistent on that quite some time, and I’ve made my views known to the Chief Executive Officer of the HSE who has undertaken to ensure there would be uniformity across the system,” he added.
“Clinical autonomy applies but I don’t think it was appropriate that partners were denied access but then media were allowed in .
“I think there has to be consistency in terms of decision making, but I’m not privy to the clinical decision making in respect of the Rotunda, but I do think there has to be consistency.”
Mr Martin said he also understood the anger from parents.
“I believe that you can’t have one set of guidance for partners, and another set of guidance then for media,” he added.
In a statement, a spokeswoman for RTÉ said that the film crew was reduced to “the bare minimum” with a lot of filming taking place off-site.
The spokeswoman added: “For filming this season, we reduced our footfall in the hospital to the bare minimum with a lot of filming taking place off-site.
“The majority of filming in the hospital was recorded by remote cameras controlled from outside the building.
“Additional research and filming was produced by a single person or on occasion by a compact two-person crew.
“Strict Covid-19 infection prevention and control protocols were followed at all times by the production.”