UPDATED 8.43am Staff at Pukekohe Intermediate School say they were only told about a medical health scare affecting their students yesterday afternoon.

Pukekohe Intermediate Dental Clinic has had a piece of equipment malfunctioning since September, the last time the equipment was found to be correctly functioning.

LISTEN ABOVE: Counties Manukau Health chief medical officer Gloria Johnson spoke to Mike Hosking

A health nurse briefed staff and assured them parents of at risk children would be notified today.

Around 2,500 children who visited the clinic between September and January may be a risk of infection of HIV and Hepitis B and C after dental equipment malfunctioned at the school's dental clinic.

Year sevens are returning to the school this morning and staff members say they're hoping for the best.

The pressurised air system that blows air, and the suction system that removes saliva somehow became connected.

Counties Manukau chief medical officer Dr Gloria Johnson told Mike Hosking screening is being offered to all of the children who've attended the clinic since September.

"The risks to an individual child are actually tiny, but clearly with the numbers involved it's a major issue, and it's going to take us quite some time to do an individual appointment with every child.

"And we will be determining what their immunisation status is. If any of them appear to have any illness of any kind that could be related to this, then we'll be offering appropriate clinical management plan for that individual."

Ms Johnson said it will take weeks to test everyone.

Medical Association chair Steven Child agrees that the the risk of contracting Hepatitis and HIV is extremely low.

"One in 100,000 children may have an infection, and then there's a 1 percent chance they spread it on to the next patient.

"It means you could be looking at a one in a million - 10 million chance that you've passed any infections on through this."

Mr Child said the malfunction "allowed fluid to spill in the equipment that was being used on subsequent patients - in other words the clean didn't absolutely remove all fluid."

Ms Johnson said it's the largest public health scare she can remember in South Auckland.

"Certainly I'm not aware that we've had to deal with anything that involves so many children in recent times."

Parents turning up to Pukekohe Intermediate this morning, say it's alarming.

"I think there needs to be a report and I think it may be a wake up call for the rest of the school dental surgeries," said one mother.