She said the number of people hospitalised would unfortunately grow.
McElnay said 618 people were in hospital on Sunday, but just 1.6 per cent were in ICU - so the percentages were much lower than Delta.
McElnay said there was continued pressure on staff in hospitals because of Covid-19, particularly through the night.
McElnay said there were very specialised areas where it could be quite challenging to operate services.
Critical healthcare workers can now return to work earlier than usual, but only if it can be done safely and it was needed to provide the service, she said.
Healthcare workers with two negative tests can return to work on day 6.
Covid-19 positive staff can return to work on a Covid ward as long as all patients have coronavirus. They must wear N95 masks, be asymptomatic or have mild symptoms, agree to return, and work in a situation where their absence puts an essential service at work.
At this stage, she was not aware of any asymptomatic Covid-19 positive healthcare workers working. By only working in a Covid ward, there was no risk to the patient from a coronavirus point of view, she said.
That option should only be used when all other options had been exhausted.
McElnay said a system had been in place that would allow some healthcare workers to return to work early with a negative RAT at days 5 and 6.
The ministry was asked to provide a pathway for a situation where there were a lot of Covid cases on a ward and staff who had tested positive for Covid were needed to care for them. They advised healthcare services about the latest option at the weekend and had lengthy guidance on this.
McElnay thanked all staff - especially in Auckland - for being flexible to keep the health system running while under pressure.
She said DHBs would have figures around how many staff were isolating.
She was aware of staff being moved around to cover the most important duties.
Staff with Covid who were returning to work should not feel pressured, she said, and DHBs had been discussing this with unions.
The MoH had also requested a daily check-in with staff and said any staff feeling stressed should be sent home.
Today's cases
Today's new community cases are in Northland (718), Auckland (9881), Waikato (2146), Bay of Plenty (1691), Lakes (660), Hawke's Bay (707), MidCentral (632), Whanganui (166), Taranaki (525), Tairāwhiti (366), Wairarapa (136), Capital and Coast (1787), Hutt Valley (1061), Nelson Marlborough (435), Canterbury (1903), South Canterbury (129), Southern (914) and West Coast (30). Seven are as yet unknown.
There were 19 cases at the border.
There are 192,452 active community cases. In total there have been 263,448 cases in New Zealand.
Of today's cases, 23,298 were identified via rapid antigen testing and 596 were identified via PCR testing.
A decrease in numbers over the previous days was most likely a result of low testing or low self-reporting of RAT test results at the weekend.
The seven-day rolling average of cases was 18,669. Between March 1 and March 7, this figure rose by more than 7000 and hospitalisations increased from 373 to 696.
"These numbers clearly show that Omicron is still spreading in our communities. We all need to continue to wear a mask, physical distance, and get tested where required to reduce the spread of the virus."
The ministry reported that they continue to see a larger proportion of unvaccinated cases in hospital.
In Northland and Auckland hospitals, 19.4 per cent of those over the age of 12 with Covid-19 and for whom MoH has vaccination data, have had no doses of the vaccine.
Just 3 per cent of eligible people aged 12 and over in New Zealand have had no doses of the vaccine.
The ministry said unvaccinated people were significantly over-represented in hospitalisation rates.
"The numbers send a clear message: getting vaccinated will help to keep you out of hospital if you catch Covid-19 and could save your life."
In the past seven days, 12.2 million RATs have been dispatched.
Yesterday, 265 first doses of the vaccine were administered, 609 second doses, 41 third primary doses, 10,450 booster doses, 608 paediatric first doses and 310 paediatric second doses.
The assumption at the moment was that all the current cases were Omicron, McElnay said.
Whole genome sequencing was the only way to tell the variant and because of the sheer number of cases they weren't able to do this with all cases, just those in hospital.
The last report she had seen showed the vast majority of cases were Omicron. Delta cases haven't been seen for some days. Only hundreds of cases were being genome sequenced at the moment.
RAT approval process
The MoH had a process in place to approve RATs and the process had been recently reviewed to look at the criteria for approvals, she said.
On the basis of that review, the MoH had gone back to suppliers and asked them to provide more information. If that information was acceptable then they would approve more - and she believed this would happen.
The system was in place to make sure RATs did what they said they would do on the packet and were as accurate as possible.
"I'm confident we will see more RAT tests approved."
Yesterday's Queenstown vaccine temperature botch was a cold chain issue, McElnay said.
She the vaccine cold chain needed to be maintained to make sure it was kept at the correct temperature.
She said it was unfortunate it happened, and apologised to the individuals who were vaccinated and had since found out it may not be as effective as they thought it would be.
On new research, New Zealand had seen a very low number of deaths because of Covid compared with overseas, she said.
The ministry was looking at the broader effects of Covid in the longer term. Chief clinical officers were looking at the latest insights, as well as working with the University of Wellington to establish research about the impacts of Covid in New Zealand.
She said people could play their part to prevent the spread of the virus and make sure the healthcare system could cope with demand.
She encouraged people to report their test results and to get tested if they had symptoms.
The "basics" such as social distancing, good hygiene and wearing masks also worked, she said.
Michael Dreyer, the ministry's group manager of data and digital, said the system could now handle 20,000 cases an hour. The RAT requester site is now fully operational and yesterday 55,000 orders were placed.
He asked people to record their result on My Covid Record, whether it was positive or negative. It helped provide a clear picture about how the pandemic was progressing.
From March 10, the ministry will send text messages telling people when their isolation period is completed.
He encouraged people to use online services because they were quick to use and took pressure off call centres.
Hipkins on possible isolation, mandate changes
Speaking later in the afternoon, Covid-19 response minister Chris Hipkins said he was considering advice on whether isolation can be reduced.
Hipkins was also asked about what will happen once NZ's Covid numbers plateau.
"We haven't had our peak yet, he said.
"There will be plenty of time to consider changes to the traffic lights or vaccine mandates."
Overall case numbers are still on the way up.
"We've been working with Auckland hospitals, they've said pressure has eased. But we're looking how to help."
He said he didn't know how many staff were sick with Covid.
He had full confidence in hospitals being able to manage infection control and keep staff safe.
Finance Minister Grant Robertson was asked if a worker would have to use their full 10 days of sick leave or if they could get Covid leave support.
"We want people to be able to recover and recover well and not undermine future needs if they're sick," Robertson said.
"Clearly we put the scheme in place so workers can stay home when they're sick."
25,000 school staff, pupils isolating
More than 25,000 school staff and students across New Zealand are thought to be isolating with Covid-19 as the virus creeps into about 60 per cent of the country's schools.
Yesterday, Prime Minister Jacinda Ardern said hospitalisations were being tracked, but these numbers might lag about five days behind real peak cases.
Numbers were rising in northern regions, where Omicron was expected to peak first.
"We're not there yet. We're doing the policy work to be prepared, regardless," the PM said.
Yesterday, 17,522 new community cases of Covid-19 were reported.
There were 696 people in hospital yesterday, including 13 in intensive care.
Covid-19 was reported for the first time in the Chatham Islands.
Emergency ambulance services nationwide meanwhile recorded the highest-ever 111 call volumes over the weekend.
At its peak on Sunday, St John and Wellington Free Ambulance recorded 2322 calls into its Auckland, Wellington and Christchurch centres - about 100 more calls a day than the previous record.
Even mild infection may be bad for brains: Scientists
The data will be released after scientists revealed today some of the strongest evidence yet that Covid-19 can harm our brains – particularly in areas linked to smell and memory.
But they caution that more investigation is needed to understand whether the clear pattern they found among the hundreds of UK people studied did indeed mean long-term damage.
In one of the largest studies of its kind to date, and published in scientific journal Nature, a team of researchers led by Oxford University's Professor Gwenaelle Douaud analysed changes in the brains of 785 participants in the UK Biobank.
People in the study had two brain scans around 38 months apart, and also underwent cognitive tests.
A total 401 participants tested positive with mostly mild Covid-19 infection between their two scans, while the remaining 384 non-infected people were used as age and sex-matched controls for the study.
When the researchers compared those two groups over time, they found "significant, deleterious" long-term effects among those people infected with the virus: notably a reduction in grey matter thickness in regions associated with smell and memory of events.
They also observed tissue damage in regions linked to smell, while post-infected people showed larger cognitive decline than controls between scans.
"On average, the participants who were infected with Sars-CoV-2 also showed greater cognitive decline between their two scans, associated with the atrophy of a brain region known as the cerebellum, which is linked to cognition," the researchers said.
"The findings may indicate the degenerative spread of Covid-19, either via smelling pathways, inflammation of the nervous system or a lack of sensory input owing to a loss of smell."
Importantly, the documented effects were still seen after excluding the 15 people who had been hospitalised with Covid-19 - implying even mild illness may have consequences for the brain.
