The Dunedin Community Salmon Trust hatchery in Sawyers Bay was broken into last weekend and the aerators were turned off, resulting in the death of about 200 salmon.
Trust chairman Steve Bennett said he could not understand why someone had jumped a barbed wire fence and switched off the aerators.
"There is actually no benefit for anyone from people killing all these fish."
The 3-year-old salmon, each weighing between 6.75kg and 9kg were due to be harvested for their eggs to build next year's release.
"Those were our broodstock, so they were 3-year-old fish we were going to strip the eggs off and the eggs would then create next year's batch of smelt we would use for release."