Professor Robert Booy, Head of the Clinical Research team at the National Centre for Immunisation Research and Surveillance (NCIRS), described the figures as very encouraging.
"We're at a very high level which should be engendering a lot of herd immunity. Herd immunity doesn't start at 95 per cent it starts before that and we are doing extremely well right across the country," Professor Booy told AAP.
"There is a small amount of variability but not to the extent that is worrying," he added.
Herd immunity is a form of immunity that occurs when the vaccination of a significant portion of a population - or herd - provides a measure of protection for individuals who have not developed immunity.
When high levels of a population is protected through vaccination against a virus or bacteria, it becomes difficult for disease to spread because there are so few susceptible people left to infect.
Analysis of immunisation records across Australia's 31 Primary Health Networks (PHN) found the proportion of fully immunised five year olds was highest in Western NSW at 96.0 per cent.
The North Coast in NSW and Perth North had the lowest rates at 90.6 per cent.
"'We're not surprised to see lower rates in places of like the North Coast of NSW and improvements are happening right across the board," said Prof Booy.
The number of teen girls to have received the HPV vaccination, ranged from 85.6 per cent fully immunised in Central and Eastern Sydney to 69.2 per cent in Tasmania.
For boys, rates ranged from 83.5 per cent in Murrumbidgee (NSW) to 62.5 per cent in Tasmania.
Professor Booy said these are "superb" figures.
But despite the encouraging improvements in vaccination rates AIHW spokesperson Tracy Dixon said it was important the community does not become complacent.
"We need to maintain high immunisation rates to protect the vulnerable groups in our community,' Ms Dixon said.
Explore the immunisation rates in your area