He said one of his most intense frustrations in NZ had been working to achieve the target, only for that work to be undone "because we are not going to meet a year-end budget".
"When we hit winter last year, there was an urgent need to meet the bottom line of the budget and as a result there was a recruitment freeze, and as a result of that some of the ward staffing was less than ideal and because of that, the emergency department was gridlocked again. We went backwards," Dr Parke told the Weekend Herald.
This would have led to spending extra money on patients staying in hospital for longer than they would have if the policy was being met, he wrote in a blog.
"Some patients will again have been put at risk of avoidable harm during this period."
The Auckland District Health Board had been at 95 per cent for the emergency department target since the July-to-September quarter in 2011, but dropped to 92 per cent for the same quarter last year.
"What's frustrating for us is going hell for leather on one target and then suddenly you get derailed. And then you have to pick it all up again.
"We've actually hit 95 for the quarter to the end of December, because the freeze came off and winter stopped," Dr Parke said.
But board chairman Lester Levy said missing the target by 3 percentage points was relatively minor.
He said that in March, the board learned it was heading for a $15-20 million budget deficit, which led to money-saving changes, and the financial year ended with a small surplus.
Talk of a recruitment freeze was a misinterpretation; more appointments were approved then than in the corresponding three months of 2011, Dr Levy said.
"There was more scrutiny on replacing positions over April-May-June; there was no recruitment freeze. In February, there had been a short freeze."
But the chairman of the New Zealand faculty of the Australasian College for Emergency Medicine, Dr John Bonning, and Health Ministry emergency department target "champion" Professor Michael Ardagh, shared Dr Parke's concerns about the effects of financial targets on clinical targets.
Dr Bonning said: "From time to time some DHBs have been given more funding for certainly senior medical officers in emergency medicine but some have suffered from recruitment freezes."
Professor Ardagh said fixing the whole-of-hospital problems that caused gridlock was good for patients and DHB finances.
Health Minister Tony Ryall said it was up to DHBs how they used their extra funding to improve services within budget but he expected them to put frontline services for patients first.