The new system has seen Territory vaccination rates fall by about seven per cent for first doses and six per cent for second doses.

It's not fair or accurate, says Police, Fire and Emergency Services Minister Nicole Manison.

Under the new system, 82,018 people or 43.04 per cent of the eligible population aged 16 or over have been given their first jab.

And 48,979 people or 25.7 per cent are fully vaccinated, according to the Commonwealth Health Department on Friday.

But the NT says the figures are wrong.

The actual number of eligible Territorians who have been given their first dose is 96,077 or 50.4 per cent of people aged 16 or older, with 59,820 or 31.3 per cent fully vaccinated.

"We believe the way we are reporting it is the best, most transparent and accurate way to report how vaccines are tracking," Ms Manison said.

The Commonwealth's new method uses the address of each person vaccinated as identified on their Medicare card.

However the NT is counting the actual number of people jabbed as a percentage of the 190,571 eligible people the Australian Bureau of Statistics estimates is in the NT.

It's the same method the Commonwealth was using until the recent change, which is understood to have happened between July 25 and August 1.

"The way we're counting this is making sure we recognise what we see as the actual numbers community by community," Ms Manison said.

"If you just rely on Medicare records alone on who has been vaccinated ... It's not the fairest and most accurate way."

The high proportion of transient residents who live and work in the NT but have an address in another state listed on their myGov online accounts has caused the disparity, a Commonwealth Health Department spokesman said.

NT Health Minister Nicole Fyles said it's unclear why the federal government introduced the new method.

The Commonwealth Health Department has been contacted for further comment.

Australian Associated Press