The identification comes just weeks after Fish and Game released about 3500 trout from the hatchery into 10 reservoirs and lakes in Otago as part of its regular stocking programme.
Otago Fish and Game manager Niall Watson said those fish were released in September and had no signs of illness.
"No [further] fish liberations will proceed until the situation is clarified," he said.
There have been concerns about the possibility of the Aeromonas bacteria spreading from the Mataura River, near Mataura, where the sick lampreys (kanakana) were first discovered last month.
The hatchery manager found a poor-conditioned trout with lesions at the hatchery last week and sent it to the Ministry of Agriculture and Forestry (Maf) for testing.
Maf biosecurity response manager Glen Neal said the trout was the only fish affected among the thousands being raised in the hatchery's stock waterways for recreational fishing.
"The detection of this strain of this bacteria in a trout is, unfortunately, not unexpected. This has not been found in any other species to date."
The bug was known to affect a range of fish including trout, eel, salmon, whitebait and kokopu.
It was a difficult process to identify the particular strain of the bacterium, which had not been found in New Zealand before, he said. It did not pose a direct risk to human health but eating fish that appeared unhealthy was not recommended.
Two other fish with suspicious markings had been sent for analysis but there had been no further deaths. The other 3000 trout appeared healthy, he said.
Fish and Game had stepped up monitoring of the hatchery stock and had restricted access to staff involved in essential management, he said.
Maf was asking anglers to report any dead or ill fish and reminding them of the importance of checking, cleaning and drying equipment and clothing when moving between waterways.
