The National Health Performance Authority report released on Thursday found in 2012, 75 per cent of 15-year-old girls had completed a three-dose human papillomavirus vaccine, above the national average of 70 per cent.

The report also found that almost a third of children in Byron Bay did not have up to date immunisation, and only 82 per cent of children in south Canberra were fully immunised.

More than 95 per cent of two-year-olds in Gungahlin were recorded as fully immunised and one-year-olds in Weston Creek achieved one of the highest immunisation rates at 94.8 per cent.

Belconnen recorded 94.6 per cent in the same category.

Chief Minister Katy Gallagher welcomed the results but said the government would continue to focus on two-year-old Aboriginal and Torres Strait Islander children in the ACT due to results below the national average.

''Once the levels get to below 80 per cent in a particular community, your herd immunity is challenged and therefore it gives the opportunity for some of these illnesses to come back … and for vulnerable groups, it can threaten their lives,'' she said.

''Where we do see deterioration in our performance, we go and look at how we are getting our information out and work with GPs in particular to address any deficiencies.

''I don't think we are complacent at all.''

She said advice from the ACT Health Directorate suggested between 3 per cent and 5 per cent of parents did not vaccinate their children.

Nationally, the report found the number of children not fully immunised had fallen by nearly 2000 to 75,000 in 2012-13.

Of these, a total of 15,000 children were registered as ''conscientious objectors''.

Children registered under conscientious objector provisions are highest in Queensland's Sunshine Coast region at 7.1 per cent, and at 0 per cent in far-west NSW.

"The ACT immunisation coverage rates for Aboriginal and Torres Strait Islander children was above the national average in two of the three age cohorts,'' Ms Gallagher said.

The biggest improvement in Australia-wide immunisation rates was recorded in five-year-old children, reaching 91.5 per cent.

Children should have completed immunisation by five years of age.

NHPA chief executive Diane Watson said the data would assist health professionals to target areas in need of higher immunisation rates.

"Through local-level reporting, we can clearly identify areas in Australia with low rates of childhood immunisation,'' Dr Watson said.

"This information can be camouflaged by national, state and territory level reporting."