The Irish Dental Association (IDA) has said that every year 10,000 children under the age of 15 are being admitted to hospital to have teeth removed under general anaesthetic.
The association has described the problem as a national disgrace.
However, Minister for Health Leo Varadkar told RTÉ's Morning Ireland that the figure seemed high.
He said he believed there were 3,600 admissions to hospital, not the 10,000 quoted, and the 3,600 figure may be an over estimate.
According to the IDA, around 200 children a week are being admitted to hospital to have teeth removed with many of them undergoing multiple extractions.
It states the rate of hospitalisations could be five times higher than that in the UK.
The association is blaming cuts to free dental health care and said the figure was an indictment of previous and successive government slash-and-burn health policies.
It says waiting times for young children with chronic dental infections were now up to 12 months.
The IDA says around 3,000 children are currently waiting to undergo general anesthetic for dental surgery.
However, the HSE has rejected the suggestion by the IDA that 10,000 children are receiving general anaesthetic for dental extractions.
The HSE believes this figure to be in the region of 3,600 a year.
Sinn Féin Senator Kathryn Reilly said there needs to be more funding to ensure children's dental health is looked after.
"The IDA has credited government cuts to family dental supports since 2010 as the cause of children having to be hospitalised to have teeth removed," Senator Reilly said.
"These cuts combined with the constant undermining of what had been a highly effective schools screening service and the fact that too many of our young people have a diet containing too much sugar has meant that these services should be expanding not contracting.
"In order to make sure our children's dental health is looked after, the free dental care programme needs to be properly funded."
In a statement, the HSE said it is planning a national audit on general anaesthetic waiting lists for children and for those with special care and special needs.
There are 305 dentists employed currently in the Irish public service, the HSE said.
It added that dental services in the HSE have recommenced recruiting since 2013. In targeted areas throughout the country, resources have been released to speed up this process.