Four Hyde & Seek crèches in Dublin will have to close by 31 December on foot of an order by Tusla to remove them from the register.
The crèches are at Tolka Road, Shaw Street, Millbourne Avenue and Glasnevin.
Tusla said public funding will end on the removal date and Hyde & Seek has 21 days to appeal the decision.
The child and family agency also said that it would now be publishing announcements of de-registrations on its website to give parents more information.
Tusla said it acknowledges that parents will find themselves in a difficult position to find alternative childcare.
It said it "has notified the Department of Children and Youth Affairs of our concerns, who are working with the local City/County Childcare Committees to make support available to parents".
A spokesperson for Hyde & Seek said they do not accept the "outcome of the regulatory process" and will appeal the decision to close the four creches.
"Since the airing of the RTÉ programme we have continued to work to ensure we adhere to the highest standards. We are very confident in the service provided at all four of our creches and will appeal this decision," they said.
Last week, it emerged that a number of members of a new management team put in place at Hyde & Seek Childcare following an RTÉ investigation into care standards at the Dublin crèche chain resigned their positions.
RTÉ Investigates: Crèches, Behind Closed Doors, which was broadcast in July, went undercover to look at standards of care in the company.
Some of those issues observed include the failure of Hyde & Seek management to ensure staff were garda-vetted before working with children.
Minister for Children Katherine Zappone said: "The de-registrations are evidence of Tusla's robust approach in taking action where it finds evidence of non-compliance with regulations."
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Minister Zappone said she had great sympathy for parents affected by the closures.
She said: "In addition to the distress already caused to parents by the poor standards evidenced, the prospect of losing their crèche is clearly a major worry for these parents.
"Officials in my Department have been liaising with Dublin City Childcare Committee and Fingal County Childcare Committee, to offer supports to parents who will be affected by the closures."
The department said both Dublin City Childcare Committee and Fingal County Childcare Committee will extend their opening hours to support affected parents.
Brian Lee, the Director of Quality Assurance at Tusla, has said that the decision is a "very clear indication" regarding Tusla's view of the situation.
Speaking on RTÉ's Six One News, he said the decision was based on quality and safety concerns.
"We have made the decision to remove the service from the register, which is based on a decision that we are not assured that the quality and safety of the service is within requirements in terms of the regulations.
"The decision that we've made today is certainly a very clear indication regarding what Tusla's view of the situation is".
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Contact details and links to websites of all local City/County Childcare Committee can be found on www.myccc.ie
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