ACT Health said Canberra's first dose rate had ticked over 99 per cent by Thursday evening, based on Treasury population estimates from June.

That figure used Australian Bureau of Statistics' 2016 census data as its base, before factoring natural increase and changes in overseas migration.

But as the territory streaked towards full coverage, slight inaccuracies inevitable in all projections have raised the likelihood of its official rate going beyond 100 per cent.

Commonwealth vaccination rates were determined by comparing jabs logged on the Australian Immunisation Register to 2019 population estimates from the Australian Bureau of Statistics.

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The Commonwealth has stopped reporting specific percentages above a 95 per cent threshold to avoid anomalies caused by lags in population data.

"As the ABS Estimated Resident Population does not pick up real-time changes to the population, these coverage rates can exceed 100 per cent," a spokesperson said.

They conceded the inability to track real-time population shifts could particularly skew figures in specific age ranges, but said the states and territories had overall been consistent in their reporting.

Given ACT Treasury in June projected the territory's population at 431,826, that would leave just 4300 residents without a first dose at most.

Commonwealth data showed ACT first dose rates exceeding 95 per cent in every age group 25 years or above. But the figure plunged to just 78 per cent among 20- to 24-year-olds.

Chief Minister Andrew Barr on Wednesday played down the prospect of the ACT's official rate exceeding 100 per cent, saying an underestimation of the over-50 population was negated by an overestimation of the 20 to 24 range.

"I think the two are balancing each other out, so our 98.5 [per cent] is a genuine 98.5," he said.

"It's not a statistical quirk, because they've estimated we've got more university students than we actually do at the moment."

ACT Health estimated NSW residents accounted for roughly 12 per cent of vaccines administered in the territory.

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State and territory coverage figures were tethered to a patient's Medicare account, meaning those living in Queanbeyan but vaccinated in the ACT were added to the NSW tally.

But using Medicare accounts relied on up-to-date addresses, which could pose particular problems among more mobile young populations.

Australian National University demographer Liz Allen said the ACT's data did appear to reflect where vaccine recipients actually lived. But she warned comparing vaccinations to population estimates came with drawbacks, particularly if they were outdated.

"It's not surprising that the government would choose a data point and stick to it: it avoids the constant movement of targets," she said.

"[But] the trouble with locking in a [population estimate] base for the vaccine rollout is that data in areas with great change becomes potentially intolerably inaccurate the further it is from census."

Dr Allen said the territory's population had "changed markedly" since COVID-19 began.

"Thousands of people have left the territory recently, specifically overseas migrants and international students who tend to be in prime working ages," she said.

First dose bookings in the ACT have petered out over the last month, as the territory ran out of people needing their first jab. In the week beginning September 13, there were 15,561 first dose bookings made via the ACT's mass vaccination clinics and walk-in clinics at the AIS. That dropped to just 3161 in the week beginning October 4.

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