ACT Health is seeking advice on why only 70 per cent of 15-year-old girls were immunised against the human papillomavirus during 2013.
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A National Health Performance Agency report released on Thursday found the number of immunised teens dropped 5 per cent in 2013 to below the national average
An ACT Health spokesman said the department was liaising with the National HPV Vaccination Program Register to better understand the reasons for the drop in coverage.
"Although the ACT achieved good HPV coverage rates for girls aged 15 years in 2012, this slipped slightly below the national average in 2013 by 2 per cent," he said.
"It is possible that data on some doses administered in general practice were not recorded on the register.
"A policy of delivering an HPV vaccination notification form with all HPV vaccine deliveries to general practices was initiated in 2014."
The NHPA report found immunisation rates varied dramatically nationwide, from as low as 56 per cent in south-east Tasmania to as high as 94 per cent in Mackay.
"Almost three-quarters of girls (72 per cent or 99,011 girls) were fully immunised against HPV in 2013 out of the 137,460 girls estimated to be aged 15 in that year," the report said.
"The remaining 38,449 girls were not fully immunised."
Human papillomavirus is a highly contagious virus causes discomfort through symptoms such as genital warts, and can in some cases lead to cervical cancer.
The school-based vaccination program was introduced in 2007 for teenage girls and the program was extended to include boys in 2013.
"Vaccination is regarded as the most effective method of reducing a person's risk of exposure to the virus," the ACT Health spokesman said.
"The vaccine is provided free to all males and females aged 12-13 years as part of the National HPV Vaccination Program."
The health spokesman said students who may have missed doses at school could be immunised at general practices in Canberra if they were in year 8.
The ACT continues to have the highest childhood immunisation rate in Australia despite a growing number of parents objecting to vaccinations
According to the Australian Childhood Immunisation Register, the number of ACT parents refusing to immunise their children because of a "conscientious objection" has increased 35 per cent since March 2012.
