Chief Minister Katy Gallagher said it would be crucial to monitor immunisation rates in light of the $7 co-payment, which is set to be introduced from July next year.

The ACT has some of the best immunisation rates in the country, with figures reported in The Canberra Times last week revealing about 93 per cent of one and two-year-olds in the territory were fully immunised, compared with about 92 per cent of five-year-olds.

"The health of the community depends on a strong vaccination program and that parents take their kids to get vaccinated," Ms Gallagher said on Tuesday.

"I think one of the issues we will have to monitor, and there is a level of anxiety in the primary care sector about this, is what changes might flow from a co-payment being introduced.

"We don't want to see any disincentive for young families and their babies not to be vaccinated."

Winnunga Nimmityjah Aboriginal Health Service chief executive Julie Tongs said there had been some fantastic progress in improving vaccination rates for Aboriginal and Torres Strait Islander people, particularly in the past 15 years, and she was deeply concerned about the impact of the $7 co-payment on that progress.

Ms Tongs said babies needed at least four visits for immunisations in their first 12 months, in addition to other check-ups, postnatal checks for their mothers and any other health issues.

There have been 727 childhood immunisations in 329 visits in the past year alone, and as of December, 92 per cent of Aboriginal and Torres Strait Islander children were fully immunised, Ms Tongs said.

She was also concerned about the impact the co-payment on adult immunisations, and in particular, flu shots. Ms Tongs said there had already been 400 influenza vaccinations in the past six weeks alone.

"Vaccination is an extremely important preventive measure and to have to pay $7 just to come and get your kids immunised is just wrong," Ms Tongs said.

"A $7 co-payment for people who can't even afford a loaf of bread or a bottle of milk is a huge impost. We are putting our children and people with chronic disease at risk if they're not having their vaccinations when they should.

"It (vaccination) is important not just for the individual but as a protection for the whole community as it reduces transmission of vaccine preventable diseases."

Federal opposition health spokeswoman Catherine King is deeply concerned about what the $7 co-payment may mean for vaccination rates.

"GPs are the cheapest end of the health system. Governments should be encouraging people to see their GP to stay well, not putting barriers in place that will restrict access and lead to people becoming sicker," Ms King said.

"These changes will lead to worse health outcomes and cost the system more."

The Chief Minister said about 60 per cent of vaccinations were done in general practice and there were legitimate concerns the co-payment would make parents think twice about taking their children to the doctor for vaccinations.

Australian Medical Association ACT president Liz Gallagher, who is not related to the Chief Minister, said there were concerns the co-payment could affect vaccination rates.

"The immunisation program within Australian and within the ACT is world class," she said.

"There will be parents who are deterred to take their children to the doctor's when they are sick if they can't afford that $7 co-payment and therefore one would assume if they can't afford to take their kids to the doctor when they're sick, they can't afford to take their kids for routine visits when they're well either."

The Chief Minister said she was already hearing reports from doctors of declines in patient presentations since the federal government announced the $7 co-payment.