Crayfish in the Hauraki Gulfs' Leigh and Tawharanui reserves are down 25 per cent from 2014.
The decline in the reserves are due to surrounding fishing pressures, according to Dr Nick Shears of the University of Auckland.
Dr Shears, also a Marine Biologist at the Leigh Marine Laboratory, said the offshore fishing boundaries of the reserves should be extended.
"To more effectively protect crayfish and other resident animals within their home ranges, the offshore boundary of the Goat Island reserve - and similar-sized reserves at Tawharanui and Hahei - would need to be extended from the current 800m to 3km offshore," he said.
Scientists found earlier this year crayfish numbers inside Goat Island reserve were lower than when established in 1975.
These numbers were found in a recent University of Auckland survey, and were discussed at this month's Hauraki Gulf Forum meeting where concern was expressed.
The Forum chairman John Tregidga said he expected the Hauraki Gulf Marine Spatial Plan to address these issues at the end of this year.
The Ministry for Primary Industries told the Forum it is aware of on-going concerns regarding decline in the reserves.
The Ministry reduced the commercial catch limit in 2014 and the fishing industry has voluntarily made further reductions to commercial catches this year.
The Ministry also said it would carry out a full scientific assessment of the fisheries management area next year, which will act as a base for further management review in 2017/18.
It will also review whether numbers of lobsters have increased following the catch reductions.