Faculty of Dentistry dean Prof Greg Seymour said the dental school was already overwhelmed by school dental service referrals.
Nine hundred people were on the referrals list and he was concerned the new system might exacerbate the problem.
The faculty recently launched an investigation into the treatment of a 4-year-old Dunedin girl, who had five teeth extracted under a general anaesthetic as a result of initial delays in treatment for a cavity.
The girl's mother, Kirsten Powell, said daughter Samantha had her annual check-up with a dental nurse at their local primary school last September, when it was discovered she had tooth decay.
She was referred for treatment at the dental school's paediatric unit and after contacting the dental school, she was told there was a long waiting list and it might be Christmas 2008 before she was seen.
"Christmas 2008 came and went, and by the end of January there was still no appointment."
Ms Powell said she contacted the School of Dentistry several times during the following months and was told Samantha was "on the list" and to be patient.
However, seven months later, when Samantha began complaining about pain from her teeth, Ms Powell decided to "rattle cages".
"She eventually received treatment after I had to present her at the dental school in pain to get any action and, as a result, she now has had to have five teeth removed under a general anaesthetic.
"Had I not made that visit out of sheer frustration of the waiting system, and the fact that she was in pain, Sam would still be waiting for an appointment and one would have to wonder at how many more teeth would have had to be removed had she not received the treatment when she did."
Ms Powell said the length of time it was taking to get an appointment once a child had been referred by a school dental nurse was"beyond a joke".
"It is my belief that the dental system for our children is already at crisis level and the ODHB's plan to centralise it can only add to this.
In a letter to Ms Powell, Prof Seymour said he regretted she had had an "unfortunate experience" and advised her that in response to her concerns, an investigation was being carried out into how children are handled from their first contact with the school and the way in which staff manage patient inquiries.
Prof Seymour told the Otago Daily Times the dental school was being put under increasing pressure by school dental service referrals.
"On average, the waiting time to see these patients is about 10 months.
"If a child is in pain, they are seen within 48 hours, irrespective of the waiting list."
"We will have to give it [the new system] a chance and see what happens.
"But we will be concerned if the system does lead to increased referrals because it will lead to longer waiting lists," Prof Seymour said.
The ODHB Community Oral Health Service has announced all school dental clinics will be closed and a new "hub and spoke" model established.
The model has centralised clinics being placed in civic communities with mobile clinics servicing the surrounding rural areas.
At the moment, school dental clinics check children's teeth and provide education about dental hygiene.
However, if any dental work, such as fillings or extractions, is needed children are referred to the dental school's paediatric unit.
Prof Seymour said in order to cut waiting lists, the faculty needed more operating theatres, more anaesthetists and more funding for people to do the treatments.
"We are doing the best we can with the resources we've got."
