There are now calls for a national strategy to address what the report says is under-immunisation among the refugees.
Australia has one of the most comprehensive immunisation programs in the world.
But many of the thousands of refugees who arrive each year are under-immunised before they resettle and remain so afterward.
A University of New South Wales report into immunisation policy for the refugees has found inconsistency between states and territories and poor integration of services.
The study's lead author, Dr Abela Mahimbo, says a lack of data means it is hard to determine exactly how many are missing out.
"So it's actually difficult to say at that level nationally what the coverage is, but, according to small studies, they have shown refugees are under-immunised for a lot of vaccinations given in Australia."
In the past decade, more than half of Australia's refugees have come from Iraq, Sudan, Myanmar and Afghanistan.
Unrest in those countries disrupts health services, making them more susceptible to vaccine-preventable diseases.
Dr Mahimbo says, even if people have been vaccinated in another county before leaving, it is unlikely the schedule met Australian standards.
"Recent refugees that are coming from Syria have been shown to have very good immunisations, but the fact that their schedule is not as comprehensive as that of Australia reflects the need to ensure they are immunised adequately to Australian standards."
Her research has found mainstream health services and specialised resettlement services need to work together better.
"So there was just this lack of integration and coordination between these groups, leading to gaps and people just slipping through the cracks."*
The report found a need for a unified national approach to lift immunisation rates among refugees.
At the moment, only New South Wales, the Northern Territory and Western Australia have developed refugee-specific policies.
In the Australian Capital Territory and Victoria, refugees are recognised as an at-risk group but there are no policies in place to address the issue.
For Queensland, South Australia and Tasmania, there is little evidence to suggest it is being acknowledged at all.
One issue has been addressed.
Earlier this year, for the first time, the federal government provided funding for catch-up vaccines to refugees of all ages.
Royal Australian College of General Practitioners president Bastian Seidel has welcomed the funding.
"This is a really good start, but we need to make sure that the catch-up programs are administered consistently in all states and territories."
Dr Seidel says that is not easy to correct.
"Nowadays, vaccinations are administered in community health centres, in refugee centres as well, and, again, the recording often doesn't happen. So it's important to make sure we get refugees in to see a GP they trust, a GP they can form a professional relationship with."
