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Associate Prof David Gwynne-Jones, of Dunedin, said he spent more time explaining the system to patients than talking about the operations themselves.
A backlog was not being cleared, orthopaedic surgery volumes as a whole were increasing, but hip and knee operation numbers remained largely static.
''It's very frustrating when you have a very straightforward intervention that can transform people's lives, and instead we have to mess around sending them back and forwards [to be] re-scored... instead of just getting on and fixing them,'' Prof Gwynne-Jones said.
Many patients did not meet the threshold, and some had to be told they might never qualify for surgery.
''Patients find that very hard to understand, and I spend more time trying to explain the system, than I do trying to explain the hip operation, so there's something wrong there.
''There's a backlog of cases that need to be done in order to get to a level where we can offer patients treatment when they're at an acceptable level of disability, as opposed to an unacceptable level.''
Otago patients had to be more lame, and in more pain, to obtain major joint surgery because of a number of factors, including an older population, a high proportion of farmers (who are susceptible to arthritis) and previous under-provision creating a backlog.
His analysis of the situation, published in June in The New Zealand Medical Journal, was met with a ''deafening silence'' and the situation was deteriorating ''all the time'', he said.
''The real question is: what is an acceptable level of need? And I'm told every year by the registrars who come down from Auckland that any of the patients we're rejecting would walk into an operation in hospitals up north.''
His published analysis said there was health board funding for about 390 Otago hip or knee replacements, and an additional 335 were funded by ACC or privately, leaving ''unmet demand'' of at least 73 a year.
Compared with a few years ago, fewer knee and hip joint operations were being performed.
''There have been 33 fewer major joints done in Otago in 2012-13 compared with 2006-07, a decrease of 7%,'' he said.
The national formula that determined regional funding compensated for Otago's older population, but underestimated its impact and should provide more compensation, he argues.
Health Minister Tony Ryall dismissed Prof Gwynne-Jones' concerns, saying the Southern District Health Board was performing 40% more orthopaedic operations than five years ago, including more major joint operations.
The figure included Southland operations. He rejected criticism of the funding formula.
''The current population-based funding formula, developed by the Labour government, already takes age into account.''
Prof Gwynne-Jones said Mr Ryall ''conveniently'' chose 2007-08 for comparison, when fewer hips and knees were done because of lack of hospital resources.
Mr Ryall's figures also included Southland, which last year performed more hip and knee replacements than its expected volume.
Had he chosen 2006-07, it would demonstrate Otago performed more hip and knee operations then - 33 more than in 2012-13, a 7% difference.
Those who did not qualify for surgery were shunted back to their GP. The issues in Otago were likely to be present in other areas, too, but not in all, depending on the make-up of the population.