As COVID-19 took priority, a plan to fix issues with Australia's immunisation scheme for diseases other than the coronavirus was put on hold, while the mandatory No Jab, No Pay scheme to receive family assistance payments has also gone more than five years without being formally assessed for effectiveness.

A new report found monitoring of Australia's immunisation coverage was effective, but for children about to enter schooling the coverage rate was potentially about 4 per cent lower than the official national figure of 95.1 per cent, which has increased from 90.8 per cent in 2012.

The new finding follows a planned project to identify the risks posed by unvaccinated cohorts in the population through disease surveillance that was dropped and removed from the department's most recent strategy before any signs of the coronavirus pandemic.

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By age five, the national immunisation program recommends children have shots for 13 different diseases, however only four - whooping cough, diphtheria, tetanus and polio - are needed for the child to be classified as "fully immunised".

The requirements leave out any obligation to vaccinate against chickenpox, meningococcal, measles, mumps and rubella, among others that are recommended in the first five years of life.

A child with no risk factors is recommended to have up to 39 shots in that five years under the program covering 13 different diseases that protect against an even wider arrange of potential problems later in life.

But the immunisation coverage rate requirements that Health officials use to measure how well protected Australia's children are as they enter school does not match the program, nor does it match the requirements of the mandatory No Jab, No Pay scheme.

Health officials had proposed new 12-vaccination criteria for a school-ready indicator, including all but one of the diseases in the national immunisation program schedule and providing certainty for parents that children will meet the requirements of No Jab, No Pay. A decision on whether to proceed was put on hole in 2020 to focus on COVID-19 priorities.

The audit office identified that Health officials relied incorrectly on assumptions about children having had previous doses, and did not have a consistent approach to including or excluding vaccinations.

Rotavirus, which leads to one child death annually, is the only disease included in the government's vaccine program but not a requirement at any age checkpoint.

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