A lack of data around "mystery" Covid-19 cases not linked to overseas travel has scientists concerned about the prospect of moving out of lockdown.

According to the Ministry of Health, the source of 10 per cent of the 1386 confirmed and probable cases is unknown, with community transmission believed to account for just two per cent of all cases.

But public health experts say it is not clear if those in "clusters" originated through overseas travel or community transmission.

Otago University public health professor Nick Wilson said before the country moved out of alert level 4, there needed to be "state of the art" data systems indicating exactly what was happening.

"The current data still has some way to go. We need to be able to clarify the percentage of cases that are among travellers in quarantine, the percentage that are linked to such travellers, and then those that have no link to such travellers - the community transmission."

According to the Ministry of Health, 39 per cent of cases are linked to recent overseas travel, 48 per cent contact with a known case, 10 per cent still being investigated and just two per cent was from community transmission.

But Wilson said it was unclear how many of the "contact cases" were linked to travel, or were actually community transmission.

"All those clusters, except for a few travel group ones, are really about community transmission. And this is far more important than cases in returning travellers who are now all in quarantine."

Director General of Health Ashley Bloomfield said today some of those unknown cases went back several weeks, and officials were going through all of them "rigorously" to find the source.

This had seen the proportion of unexplained cases reduce from 11 to 10 per cent since Tuesday, he said.

Until the original source was identified a "wide fence" would be placed around the unknown cases.

Wilson and several colleagues were calling for digital technologies to help ramp up contact tracing to assist with contact tracing, border controls, early diagnosis and surveillance.

They also believed state of the art testing and surveillance systems needed to be ready before moving out of lockdown, which involved thorough testing right from moderate and severe cases to asymptomatic people, through to even wastewater testing to ensure the virus has been completely eliminated.

"Without these things in place or nearly ready to go – we are risking the elimination goal not being achieved if lockdown levels are reduced," Wilson said.

"And we absolutely don't want to have to return to lockdown once it is finished – as this would be terrible for business confidence and public confidence."

Wilson said people urging the lockdown to end and comparing New Zealand to Australia and its more relaxed approach missed the point, as they were focusing on a different strategy - suppression, rather than elimination.

"So it makes perfect sense that Australia does not need such a rigorous lockdown."

Otago University public health professor Dr Michael Baker said without precise data about how many cases were from within New Zealand's communities it was not safe to move to a lower alert level.

"We need to know which cases have just arrived in the country, and have gone into quarantine, and those that have originated in the community.

"Because if we have community transmission, it is a dangerous time to be coming out of lockdown."

As New Zealanders returned from overseas the number of positive cases would likely continue to increase, and these needed to be separated from those recorded in the community.

"Looking at the data we just can't tell that at the moment."

The Ministry of Health recently said it was working to streamline information flows about clusters between themselves, district health boards and testing labs, including information around transmission routes, level of containment, timing of new cases, and proportion of close contacts traced.

Otago University infectious diseases specialist Dr Ayesha Verrall was also carrying out an audit of the contact tracing programme, which will be presented to Government ministers over the next 24 hours, before being made public.

Today's 20 new cases brought the total number of cases in New Zealand to 1386 - 728 of whom have now recovered.

The official death toll from Covid-19 remains at nine. Thirteen people are in hospital and three are in ICU.

On Monday the Government is set to decide whether to extend the lockdown for the whole country, take the country to alert level 3 or potentially maintain the lockdown in only certain regions of the country.