There are 29 new Covid cases in the community today - including a patient at Auckland City Hospital who was admitted to intensive care and then tested positive.

This is the final data Cabinet will consider before its meeting today to decide on alert levels.

Prime Minister Jacinda Ardern and director general of health Dr Ashley Bloomfield will then hold a press conference at 4pm to explain the numbers and reveal a roadmap for Auckland out of lockdown.

Twenty-eight of today's case are in Auckland and one is in Waikato, the Ministry of Health's 1pm update said.

Eight of today's cases are so far unlinked to existing cases and investigations are ongoing.

The remainder were in isolation during their infectious period.

New case at hospital ED

Meanwhile a person who went to Auckland City Hospital's emergency department yesterday and was admitted to intensive care for non-Covid reasons has tested positive.

Auckland DHB say it is working "at pace" with the Auckland Regional Public Health Service to investigate and identify any potential contacts.

"The patient was separated appropriately on arrival at the ED as being at risk for Covid-19 and staff were wearing appropriate PPE including N95 masks. They had also previously visited the ED and returned a negative test on Saturday, so it is believed the infection has been identified early.

"Auckland DHB advice is that patients and whānau who have been at Auckland City Hospital and in the ED do not need to take action unless they are contacted by public health officials."

Seven active subclusters

There are 15 epidemiologically linked subclusters - seven are active, one is contained and seven are dormant.

There are another 14 unlinked subclusters - five are active, one is contained and eight are dormant.

Thirty people are in hospital with Covid: three in North Shore, 13 in Middlemore, 13 in Auckland and one in Waikato.

Five patients are in intensive care or high dependency units.

The Waikato District Health Board says there is high demand at community testing centres in Hamilton and Raglan. Yesterday, more than 600 swabs were taken across the testing centres at Founders and Claudelands in Hamilton, and around 150 swabs were taken at the pop-up testing site in Raglan.

As a result, the DHB is advising people who don't meet current testing criteria to consult Healthline on 0800 358 5453 or your GP before seeking a test.

There have been no unexpected wastewater detections in the last 24 hours.

Wastewater testing at 14 sites in the Waikato between September 23 and 30 (including Hamilton) did not detect any trace of Covid.

Further wastewater sample collection will be done within the Waikato and Manawatū-Whanganui regions, including Raglan, Huntly, Te Kauwhata, Ngaruawahia, Feilding, Hunterville, Tokoroa, Putaruru, Hamilton and Palmerston North.

Results are expected in the coming days but the timing depends on various factors including the sample arrival times and need to re-run tests.

Personal travel exemptions for residents wanting to leave or enter Waikato's alert level 3 area will be processed by the Ministry of Health from 7am tomorrow.

The criteria for such exemptions will be the same as those for Auckland's alert level region.

In total, there are 1184 contacts being managed as a result of these outbreaks.

Of those, 19 per cent are yet to received an outbound call from contact tracers. A test result is unknown for 29 per cent of contacts.

There are 138 locations of interest as at 10am today.

In the last 24 hours, 13,693 Covid tests have been processed, including 7420 in Auckland.

A total of 27,033 vaccinations were administered yesterday, consisting of 7041 first doses and 19,992 second doses.

Of those, 12,923 were provided in Auckland.

Regarding the Auckland-based truck driver who tested positive after travelling to Palmerston North, initial negative test results have been returned from the driver's four close contacts associated with worksites of the driver, who is isolating in Palmerston North.

There are two Covid cases at the border today.

One is in quarantine aboard a ship after travelling to New Zealand from Vanuatu on Friday. They tested positive with the virus on entry. It is not clear where the ship was attempting to berth.

The other case is in a quarantine facility in Auckland after travelling from the United Kingdom, via the UAE, on September 29. Their positive result was picked up through a routine day 3 test.

More than half of yesterday's 33 cases (19) were infectious in the community and have exposure events linked to them.

So far today it has emerged that a baby has tested positive at North Shore Hospital and an Auckland taxi driver may have been infectious for two nights while carrying passengers. Taxi drivers are legally required to wear a mask in level 3.

Ardern also confirmed there are more household infections relating to the Raglan case revealed yesterday.

Meanwhile more than 2 million people have now received two doses of the vaccine, Covid Response Minister Chris Hipkins said today.

"As of this morning, 2,018,305 people were fully vaccinated with two doses, representing 48 per cent of people aged 12 and over," he said.

"This achievement is also testament to the great effort of New Zealand's health workers who've been working long and hard to deliver the largest vaccination programme in our history."

Alert level 2 unlikely for Auckland

Several public health experts have said that announcing a move to level 2 for Auckland this week would be too risky, given the relatively low vaccination rates there.

But Ardern is expected to say what aspects of alert level restrictions are lower risk and could be brought in for Auckland, as well as how the vaccination rollout can be boosted.

People line up for Covid tests at Founders Theatre in Hamilton today. Photo / Christine Cornege

The trend in cases - including unlinked cases - in Auckland has been rising in the past week. Yesterday there were 33 cases, which only included one of the two Waikato cases, and 23 of them in the past fortnight were unlinked.

This morning Ardern said the household contacts of the Raglan case have tested positive.

Genomic sequencing has linked the two Waikato cases to the Auckland outbreak, but an epidemiological link - who they caught the virus from - remains unclear.

A baby in North Shore Hospital, the parent of a baby in Auckland City Hospital, and an Auckland taxi driver have also tested positive since yesterday's update.

New locations of interest include a BP station and a sushi place in Raglan, and a Burger King in Palmerston North, following a truck driver who travelled from Auckland to Palmerston North testing positive.

This morning Ardern said there were other options than simply moving Auckland to level 2, and ministers had been considering which lower risk aspects of the alert levels might be introduced for Auckland.

She also said that high vaccination rates provided more options than chasing elimination.

She has not set any official vaccination targets, but yesterday she said that 90 per cent coverage of the eligible population would have meant the five-day level 3 restrictions may not have been needed in the Waikato.

Asked whether that meant the elimination strategy was at an end, she said: "We're in a transition. So we are changing our strategy as we move. We still need to control this outbreak but we are transitioning."

Just under 79 per cent of eligible New Zealanders have received at least their first jab, while the rate in Auckland is just under 84 per cent.

Five days at level 3 for parts of the Waikato started at midnight last night, though there was some frustration due to a boundary map only being released overnight.

The two Waikato cases, based on information so far, have not travelled outside the region, though there are some 5000 to 7000 people from outside the Waikato that visited the region during the five days that at least one of them were considered infectious.

Ardern said yesterday that she had not seen any need to put all of the North Island into level 3 at this stage.

She also all but ruled out putting Auckland back into level 4, adding that part of the moving Auckland to level 3 in the first place - described as a calculated risk by public health experts at the time - was because of the public's weariness of level 4 and the possibility of rule-breaking creeping in.