"This is a parental choice that makes it difficult for us to further improve our immunisation results," Dr Cragg said.
She said the WDHB continually strived to improve its results through the primary health and outreach teams.
"They all work tirelessly to track down children not being immunised or those who have not completed their immunisation programme," she said.
"The outreach staff visiting those who decline to immunise their children are very vigilant about doing this. Sometimes they will sit outside homes waiting for parents and caregivers to return at the end of the day.
"However, we have to respect that a lot of these families are making an informed decision and it's important we recognise that this 4 per cent only represents a handful of children scattered across the region," Dr Cragg said.
But she said the numbers not being immunised were very small and while 5 per cent declined to be part of the programme there were a further 4 per cent of children the teams had not been able to find so they could be immunised.
Janine Spence, the B4 School facilitator with the Whanganui Regional Primary Health Organisation, said not immunising put a child at increased risk of disease.
Ms Spence said while it was the parent or caregiver's choice to decide whether or not to immunise, it was important they talk to their health care provider to find out about the diseases in order to make an informed decision.
"This decision is then recorded in the patient's notes. Each time another vaccination is due the parents are contacted to see if they wish to immunise," she said.
The immunisations cover diphtheria, pertussis ( whooping cough), tetanus, polio, hepatitis B, hib (haemophilus type b) pneumococcal vaccine, measles, mumps and rubella.
For a child to be fully immunised at age two, it should have completed six-weeks, three- month, five-months and 15-month immunisations.
Ms Spence said schools, kindergartens, early childhood centres and kohanga reo kept a record of which children were and were not immunised.
"In an outbreak of disease the child who is not immunised can be excluded from the centre or school until the risk of getting the disease has passed," she said.
"Children who are not immunised are at a higher risk of getting the disease as they haven't been able to develop antibodies to protect them. They also place other children who cannot be immunised for medical reasons at higher risk of getting the disease," Ms Spence said.