Experts recommend getting vaccinated as soon as possible, with influenza yet to peak in New Zealand this year.
The new vaccine has been updated to counter several strains of influenza, including the lethal "Aussie flu", expected to hit New Zealand.
Auckland District Health Board chief medical officer Margaret Wisher said there were record-breaking numbers of adult emergency department presentations at Auckland City Hospital last winter, and this year's admissions were expected to be higher still.
"Auckland DHB is encouraging the public to prepare now for what could be a severe influenza season."
The latest New Zealand vaccine had been updated to fight four strains of the flu which had been causing trouble overseas - two "type A" and two "type B" strains.
Flu vaccinations were at their highest in the last six years, with over 1,294,907 New Zealanders vaccinated so far - an additional 77,413 more than last year.
Immunisation Advisory Centre director Associate Professor Dr Nikki Turner said the content of the flu vaccine had been changed in an attempt to head off the most likely strains.
"We're hoping it will be a better match. But flu is really unpredictable and we always have to be prepared for a bad season.
"What we do know is that flu vaccine works for individual protection but also community protection – so the more people who receive the flu vaccine, the more we can prevent flu circulating to others."
The flu vaccine was free for people most at risk, including pregnant women, people over 65 and children with a history of respiratory illness.
National Influenza Strategy Group spokesperson Brenda Saunders said it took up to two weeks after the vaccination for the body to start developing protection against the flu.
"We would recommend immunisation now, especially for those people 65+, those with ongoing medical conditions and pregnant women because they are most at risk of developing complications from influenza".
The Institute of Environmental Science and Research (ESR) monitor flu activity through visits to general practitioners, health line calls and hospitals.
"Traditionally, we see a rise in influenza cases about this time of year," Saunders said, and at the moment it was "nothing out of the ordinary".
ESR's New Zealand influenza intelligence report revealed flu had been detected in GP visits more frequently in recent weeks and influenza virus circulation was expected to increase in the next few weeks.
Saunders said some people may have the flu and not realise."Four out of five people infected do not show symptoms." This is called an "asymptomatic flu".
Health Minister Dr David Clark said he was he was pleased at the number of New Zealanders who have protected themselves from influenza this year.
"Australia and the northern hemisphere have had particularly deadly influenza seasons over the last 12 months," he said.
"More than 1.29 million doses of influenza vaccine have been distributed so far, more than any previous influenza season.
"In an average year, it's estimated influenza kills around 400 New Zealanders, many of whom have other health conditions that make them more vulnerable to complications from the disease."
Saunders said the figures showed only how many vaccines had been distributed to medical facilities but "we would like to think 1.3 million doses of vaccine have been used".
The vaccine was not 100 per cent preventation, but it was the best protection against contracting the flu this winter, Saunders said.
Immunisation Advisory Centre director Dr Nikki Turner said, "the holy grail of flu vaccines is to create a vaccine that will cover all strains and so won't need to be changed every season – the world is working hard on this one but we are still quite a few years away.
"So in the meantime, we are stuck with imperfect vaccines that are still important to use against such a nasty and common virus."
Hospitals at capacity
District health boards have raised concerns about their ability to cope should this year's flu prove more virulent than normal, with beds already at capacity.
Hospitals have been preparing for the flu season this winter, even as record numbers of vaccinations were rolled out.
Taranaki DHB spokesperson said winter was typically a busy time of year for its hospitals.
"This year exceeds last year's numbers in both the summer and winter months.
"In January, we saw a significant increase in very sick patients coming through the hospital doors every day.
"Over the last 12 months Taranaki DHB has hired 112 new nurses. Including 22 recent appointments in preparation for the increased demand over the winter months."
Whakatane Hospital experienced a dramatic increase in patients this winter, from 88.77 occupancy to 101.85 per cent. However, Bay of Plenty chief operating officer Pete Chandler, said extra resourcing was not considered necessary at Whakatane Hospital.
"We have additional bed space which is not routinely utilised, so we have extra capacity if we need it."
Waitemata DHB director of hospital services, Cath Cronin, said "during the winter months, we have all available beds open on most days".
Palmerston North Hospital has noted a decrease in bed occupancy since last year June, shifting from 107 per cent capacity to 102 per cent this June.
Though the hospital continued to be over capacity, a Mid Central DHB spokesperson said the hospital coped by placing non-resourced beds into wards and reshuffling or calling in additional nursing staff .
Mid Central DHB also increased public health notices which advised people to get the flu vaccine and to enrol at their local GP.
Rotorua Hospital and Nelson Hospital also experienced slight drops in hospital numbers this June, however both expected numbers to rise in months to come.
Nelson Marlborough Health chief executive, Peter Bramley, said, "where we see the greatest challenge in terms of occupancy is over August and September, due to admissions from winter illness".
A Hawke's Bay DHB spokesperson said occupancy numbers bumped up 1.9 per cent from last June, but this was not a result of the flu.
"Hawke's Bay Hospital experienced a busy June due to a number of major incidents, including a helicopter crash and numerous motor vehicle crashes.
"We have not seen an increase in flu-like illness, but the cold month contributed to many respiratory illnesses that needed hospital care especially in children and older people."