Tánaiste Eamon Gilmore has described allegations of poor standards of care in some creches as shocking and deeply disappointing.
Concerns were raised after footage was recorded by RTÉ's Investigations Unit which is to be broadcast early next week.
In a statement, RTÉ said the programme demonstrates that standards of childcare in three creches were in breach of HSE regulations and childcare guidelines.
The three are: Links crèche in Abington in Dublin; Giraffe crèche in Belarmine, Stepaside, Dublin; and Little Harvard in Rathnew, Co Wicklow.
RTÉ said the programme finds various degrees of mistreatment of young children in specific rooms of the creches, involving inadequate care and serious breaches of child care regulations.
No evidence of violent or sexual abuse was found.
The broadcaster said the creches involved have been given access to the footage that will be shown in the programme.
It said the findings of the investigation have been shared with the creche owners, who have been offered due right of reply.
All staff directly involved in the incidents to be transmitted have also been offered the right to respond to the findings of the programme, RTÉ said.
Gardaí and the Health Service Executive are investigating the reports.
A statement from one of the companies involved in the controversy said there was clear evidence of inappropriate conduct in caring for young children at one of its creches.
Giraffe Childcare issued the statement in relation to its Belarmine facility in south Dublin.
One member of staff had been suspended, the statement said.
The company's managing director, Simon Dowling, said he was deeply upset and disappointed by the footage provided by RTÉ.
This footage, he said, had shown unnecessary strapping of children into their chairs for purposes other than meal times, or table top activities.
Children had been seated for periods longer than necessary or considered best practice.
Mr Dowling said the company wanted to reassure every parent that it had commenced putting measures in place to correct this "serious lapse" and the company would be ensuring that all current practices and procedures were sufficiently robust to avoid these incidents ever being repeated.
Mr Gilmore said in the Dáil that the Government was deeply concerned and that the allegations tap into every parent’s worst nightmare.
Fianna Fáil leader Micheál Martin said the reports would cause alarm and distress to the thousands of parents who have their children in childcare facilities.
RTÉ said it continues to liaise with parents of the children involved, the creches, the HSE and the gardaí in relation to the programme, and any other parents who have concerns will be facilitated with a viewing of the programme before it is transmitted.
It said the production was undertaken with the cooperation and guidance of childcare experts and that "rigid production and editorial standards have been observed under the guidance of RTÉ's own journalism guidelines".