"Under the Marine Reserves Act, marine reserves should be maintained as far as possible in their natural state," said former Auckland University physicist Dr Bob White, who chairs the society.
"We are not against research in a marine reserve, but this is not the sort of research we believe is appropriate because it doesn't leave the reserve in its natural state."
But the director of AUT's Earth and Oceanic Science Research Centre, Professor John Buckeridge, said the reef was installed to enhance biodiversity in the reserve, and had succeeded.
A report last August by a research team led by Long Bay College science teacher Jonathan Jaffrey said the hollow reef balls had been colonised by Pacific oysters, green-lipped mussels, barnacles, sponges, tubeworms, sea anemones and other organisms.
Professor Buckeridge said baby crayfish also settled in the bottom of the balls where big fish could not reach them.
"We have people keen to monitor them, but they are wary of going out if DoC has indicated that they no longer have a permit."
The reef has a 35-year resource consent from the Auckland Regional Council.
ARC coastal scientist Alan Moore said he was satisfied that the balls did not harm the environment.
"We are comfortable with them being there for the duration of the consent," he said.
"The purpose of the marine reserve is for scientific research."
But Mr Fraser said DoC issued a two-year permit because AUT expected research results in that period.
"The research has merit and should continue," he said, but it needed to be well-structured and serious thought should be put into the objectives.
"I do see the value in monitoring the changes that are occurring, but in terms of arguing the point about whether the reef balls are the best things compared with any other structure that may be put into marine reserves, and whether or not marine reserves are about creating artificial structures, I'm not at all confident."
Mr Fraser said any application from AUT to extend its permit would be advertised for public submissions.
The department's Auckland Conservator, Rob McCallum, would then decide whether a new permit should be issued.
Jonathan Jaffrey et al (August 2003):
Interim report on the artificial reef constructed in the Long Bay-Okura Marine Reserve, Auckland
Herald Feature: Conservation and Environment
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