About 95 per cent of Kiwis are getting their second Pfizer vaccine jab within five weeks of their first dose.

That means of the 42,771 people who have had two doses as of Tuesday last week, about 2000 of them had their second jab more than two weeks after the recommended time to receive it.

The main disadvantage for them, according to Auckland University vaccinologist Dr Helen Petousis-Harris, is that they may have been more vulnerable to Covid-19 for longer than they otherwise would have been.

"It's not that the person's not going to have as good immunity in the long-term. It's that they might not be protected as much as they might like while that second dose is delayed."

One dose is thought to be about 70 per cent effective against symptomatic infection within three weeks of receiving it (though one study in Israel said 57 per cent) - but this jumps to 95 per cent two weeks after a second dose.

The current recommended schedule is to get the second dose 21 days after the first one, but if that isn't possible, then as soon as practicable after the 21-day mark.

Having it more than five weeks after the first dose doesn't necessarily make the vaccine less effective, a Ministry of Health spokesman said.

In fact, it recommends getting the second jab within six weeks of the first - even though it provided five-week figures to the Herald.

The six-week window aligns with recommendations from other international medicines regulatory bodies, including in the US and Australia.

• Defence Force service members told to get vaccinated or face being fired
• Ministry of Health tells Auckland GP 'we don't need you' in COVID-19 vaccine rollout
• Denmark ditches AstraZeneca vaccine over blood clot concerns
• Dozens may be missing regular COVID-19 swabs

Asked why it had provided data about a five-week window instead of a six-week window, the Health Ministry said it was taking "a conservative approach".

Petousis-Harris said the 95 per cent rate of people getting two doses within five weeks was "great".

But she urged people to get their second dose as close as possible to 21 days after their first one, which would make them as immune as possible as quickly as possible.

Those that miss the six-week window don't have to start again, she added, nor is there a reason at this stage to think a longer delay would make them less immune once they had a second jab.

"Just make sure you get the second dose as soon as possible. One dose is incredibly helpful, and does protect most people that get it," she said.

"But we absolutely need to aim for the two doses because the proportion of people that you need for population immunity - 70 to 80 per cent - is actually quite high.

"We've got to vaccinate considerably more than that [to reach population immunity] because the vaccine doesn't protect everybody."

There remain many unknowns about how effective vaccines will be over time, especially as more infectious and destructive Covid-19 variants emerge.

But Petousis-Harris said mRNA vaccines - such as Pfizer - appeared to be "absolutely phenomenal" against variants so far.

"One of the important things with the new variants is that you want to be thinking about potentially getting another dose of tweaked formulation down the track."

About half of the 9000 have received two doses.

Director-general of health Dr Ashley Bloomfield has said that purchase agreements with vaccine companies mean New Zealand will be able to access any such tweaked formulae.

Meanwhile Defence Minister Peeni Henare told Q+A yesterday that about 100 out of about 9000 Defence Force personnel have refused to be vaccinated.

About half of the 9000 have received two doses.

Those who refused the vaccine will not be working in MIQ facilities or at the border from the end of the month.

Less vaccine waste than expected

About 3 per cent of vaccine doses so far had been wasted.

That equates to about 5700 doses of the 189,000-odd doses that had been supplied to DHBs across the country as of last Tuesday.

"The Ministry of Health expects some Covid-19 vaccine discard to occur – as with any vaccine – but the number of occurrences of this is low," a spokesman said.

The amount of waste is less than the 5.3 per cent that the ministry had forecast.

"The ministry is seeing more efficient Covid-19 vaccine usage than initially predicted," the spokesman said.

"DHBs nationwide have been able to extract six doses per vial, sometimes up to seven doses per vial - more than the initially forecasted five."

There were many reasons why doses were wasted, including human error such as a vial being accidentally broken.

"The ministry is actively working to establish a clearer picture of the various and complex reasons for vaccine discard to help minimise incidents of this taking place."