The data records at least one vaccine decline among parents/caregivers whose child turned 2 between July 1 and September 30 last year.
Nationwide, this group was nearly 6 per cent, but was much higher in some regions including Northland (12 per cent), Lakes (10 per cent), Bay of Plenty (10 per cent) and West Coast (9 per cent).
The lowest decline rate was in Auckland and Canterbury DHB boundaries (3 per cent).
There were also differences by ethnicity: the decline rate was 9 per cent for Māori, 6 per cent for Pākehā, 4 per cent for Pacific and 1 per cent for Asian.
The ministry said it doesn't record which parents may later consent to their children being vaccinated, and said a small number of declines could look like large percentages if they fell within a small population.
Immunisation coverage for 2-year-olds was 90 per cent over the same period.
The data was praised as "exciting" by Dr Karen Bartholomew, director of health outcomes at Auckland DHB, during a December board meeting, saying such information "had been requested for some time", and provided a view across DHBs of vaccine hesitancy.
Border and high-risk workers are set to be vaccinated in March or April, and the general public from around the middle of the year. The Government aspires to have everyone who wants a vaccination receiving it by the end of the year.
Director general of health Dr Ashley Bloomfield last week said polling showed about 70 per cent of New Zealanders would be prepared to get vaccinated, and a further 20 per cent - the "vaccine hesitant" - would get a jab if they were very sure it was safe. About 10 per cent said they wouldn't.
It is the hesitant group that will be targeted strongly by a campaign due to begin in the next few weeks.
The Government is aiming to vaccinate 90 per cent of the population. Bloomfield said 70 per cent vaccination would be the minimum needed for herd immunity, depending on factors including vaccine efficacy.
"The key point here is the more people who are vaccinated, the more people who have individual protection, and the more likely we are to be able to get that herd immunity effect, where we stop any transmission within the community, if the virus is there."
A ministry spokesperson said planning for the largest vaccination programme in New Zealand's history "is continuing to work at pace", and a public information programme would start this month.
As well as the surveys, the ministry was using research papers and strategies from the World Health Organisation and OECD to inform this work.
"Our main focus is on providing clear, consistent access to trusted and transparent information."
Research released this week used data from the Growing Up in New Zealand longitudinal study looked at reasons for vaccine hesitancy, and found mothers were about 14 per cent less likely to immunise their young children if they were discouraged, with family having the strongest influence, followed by health professionals.
