At Middlemore Hospital last year, about 3900 patients in category two waited longer than 10 minutes, nearly 1500 more than would have been the case had the policy had been met.
Triage two includes patients with an imminently life-threatening condition, such as serious chest pain likely to be from a heart attack.
In triage three, nearly 37,100 waited more than 30 minutes at Middlemore, almost 25,000 more than allowed for in the policy.
Triage three includes those with potentially life-threatening conditions, such as moderately severe blood loss.
The other non-complying hospitals' performances were mostly better than Middlemore's, although similar numbers of patients waited longer than the recommended times.
The Starship was the stand-out, meeting triage one and bettering all other requirements.
Auckland District Health Board chief executive Ailsa Claire highlighted the median time for triage two adults to be seen by a doctor at Auckland Hospital - seven minutes, compared with the recommended maximum of 10 minutes for 80 per cent of patients.
She said doctor and clinical nurse specialist numbers had been boosted and this had reduced the median times in triage three to 38 minutes, and triage four to 59 minutes.
"Other initiatives are being planned to ensure all patients are seen within recommended times."
Auckland's three district health boards reported near-universal compliance with the Government's six-hour length-of-stay target for emergency departments.
Professor Michael Ardagh, the Ministry of Health's "champion" for the target that 95 per cent of emergency department patients are admitted, discharged or transferred within six hours of their arrival, said the triage system had become less important.
Emergency departments had moved from having a single queue to dividing patients into different areas depending on their needs.
Labour's health spokeswoman, Annette King, said the delays raised concerns about the welfare of patients. She was also concerned that the quarterly hospital benchmark reports were no longer available.
She saw nothing wrong with having the current emergency department target, but said it was becoming "a tick-box political measure".
Health Minister Tony Ryall said the six-hour target was introduced on the advice of senior clinicians.
"Increasingly, Australian hospitals are adopting a very similar ED target to New Zealand."
Delays may have been factor in death
Zachary Gravatt Zachary Gravatt may in part have been a victim of delays in triage at Auckland City Hospital.
He died there in 2009, aged 22, of blood poisoning and organ failure caused by meningococcal C bacteria.
Mr Gravatt died within six hours of his admission to hospital. He was at first diagnosed with influenza and the cause of his illness was not detected until it was too late to save him.
At 1.35pm on July 8, 2009, he arrived at hospital. At 1.43pm, he was assigned to triage category three by a nurse at the emergency department. At 3.30pm, he was seen by a doctor, coroner Brandt Shortland has written. The maximum wait time for this category is supposed to be 30 minutes.
A Nelson specialist in emergency medicine, Dr Andrew Munro, reviewing the case for ACC, identified failures in Mr Gravatt's care.
"Medical assessment took place more than 90 minutes outside of expired time for triage."
