Erindale Pharmacy had only administered 11 doses of Pfizer since November 14, managing director and ACT Pharmacy Guild Branch president Simon Blacker said.

This figure is in contrast to 2500 doses of vaccines administered since August 10.

Mr Blacker did not have figures for the total wastage of Pfizer doses across ACT pharmacies, but cited Erindale Pharmacy as an example, where four vials had been opened, but only 11 of 24 possible doses administered.

The pharmacy returned 400 doses of AstraZeneca to the federal government for redistribution on Tuesday, but is restricted from doing the same with Moderna and Pfizer doses which expire faster.

Meanwhile pharmacies have already minimised their participation in the rollout, after warning they would be forced to do so by inadequate remuneration.

Only 36 ACT pharmacies have ordered doses of Pfizer, compared with the 65 across the territory who ordered AstraZeneca and 64 who opted in for Moderna.

Contained in vials of six doses, once opened all the doses need to be administered within six hours.

Pharmacists avoid wastage by sharing around doses, only offering doses on particular days to concentrate stock and ordering in lower amounts, but are finding their efforts limited by sluggish demand.

"We were told at the start that having a dose in an arm, even if it meant the rest of the vial was wasted, was well worth the effort, so that's how we've been working," Capital Chemist Group business manager Andrew Topp said.

"And because of the minimum order quantity, if you don't open all your vials, there'll be whole vials that go to waste."

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Pfizer doses are available to pharmacies on a fortnightly basis, in lots of 120 or 240, with an expiry 28 days after their delivery.

Mr Topp said this lower threshold was still quite high for the current period: " The chances of you getting 120 patients are actually quite low."

ACT Health Minister Rachel Stephen-Smith said on Tuesday that government clinics were not experiencing the same issues with wastage, because of the ability of such clinics to deep freeze doses.

"We have significant stock on hand in our ACT government clinics, but at the moment we're not dealing with having stock expire because we have those deep freezers and we have the capacity to hold stock," she told ABC.

She said the earliest frozen stock would expire was in January 2022.

"We've told the Commonwealth government that we don't need any more supply because we have a really significant amount of stock in our freezers."

About 20,000 ACT residents are expected to become eligible for their booster doses in November, the Health Minister said, with government clinics having administered 6000.

While that cohort remains small for the moment, governments will need to play a strong role in reminding the public to take up boosters in order to mitigate further wastage, Mr Blacker said.

"There probably will come a point, if the local community don't start coming and getting their boosters when they should, after that six-month window after second dose, that doses will go to waste."

"And so a strong message for the community is: if you were early ... in the rollout, back in April, you're eligible now for your booster."

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