A child suffered a fractured leg in one creche, and childcare workers were dismissed for using sexualised language to a child in another.
Meanwhile, a creche located in Dublin was shut down, subject to garda investigations.
A total of 35 complaints were made about creches in the HSE Dublin North East area and dozens more across the country.
In one Dublin creche, a parent initiated legal proceedings after their child was found to have a fractured leg after a fall while in the care of childminders.
When the parent called to collect their child, they were informed that the child had fallen that morning. The HSE pre-school inspection team spoke with the service provider and the matter is still under investigation.
In one serious case in another creche on the north side of the city, the nature of the complaint is simply described as "behaviour management".
The creche was investigated under the Pre-school Regulations 2006 and gardai were notified. This daycare service is no longer in operation.
In another case in Carlow, a staff member was found to be using inappropriate sexualised language to a pre-school child.
The complaint was upheld and the contract of two staff members was terminated.
In the first part of a Herald investigation, details of complaints to childcare providers and follow up actions taken by the HSE were outlined and revealed under the Freedom of Information Act 1997.
Parents have raised concerns about children being hit during play, told to "shut up" by staff members and were anxious about the adult to children ratio.
In another case in Dublin, a young boy was found to be discriminated against by a childcare centre, the inspectors said that a complaint -- that the young boy did not get a place in pre-school because he is deaf -- was founded.
In Wexford, a parent complained that her three-year-old suffered a split lip which required hospital treatment and there was "no adequate explanation" given for the cause of the incident.
One concerned mum in Kilkenny removed her child from a creche when she noticed a number of inappropriate things happening.
On one occasion, the child received a black eye which couldn't be explained.
Following an investigation, the proprietor closed the service in October last year.
In this special investigation, we have outlined the most sobering comments included in the reports from parents and from HSE.
The names of children are removed from many of the HSE files because of the sensitivities of those involved.
The HSE has followed up on a number of complaints made by parents and anonymous callers.
In a significant number of cases it was found that the adult to children ratio was sufficient and that accident reporting procedures were adhered to.
But in many creches, this was not the case.