Doc freshwater ranger Pete Ravenscroft said people were cutting and driving through a fence set up to keep them out of the Kauru River, a tributary to the Kakanui River, about 15km inland from Maheno.
Rangers were trying to keep out didymo and keep the fish alive, he said. The fish had a population of fewer than 200 at its lowest point last year.
"They're the lowest we've ever seen them," Mr Ravenscroft said.
As well as the fence, other access points had been closed, the Kauru River had been closed to game fishing and it was illegal to step in the water on a 6km stretch, all measures to keep out the didymo.
But people were cutting the fence wire on a monthly basis to allow vehicles through.
"We're asking people to respect the rules in place for the Kauru, and respect the fence," he said.
The non-migratory fish, which was related to whitebait, stayed in the freshwater system, he said.
The fish had also been found near Twizel and in the Mackenzie country, but in populations of fewer than 20.
In 2007, didymo had been found in the Kakanui River, and this year had "taken off", to the point it felt like walking on a kapok mattress, Mr Ravenscroft said.
The fish needed to swim between the rocks to the sub-surface of water, and potentially could not when didymo took over.
"It they can't access that, they're in trouble."
A captive population had been kept in tanks in Concord - there had been some success breeding them - and there was funding in place to keep that going.
Mr Ravenscroft said if the didymo stayed out of the Kauru River, the fish would be saved.
Doc would also try to shift the fish to other areas, though those were limited, as they could not be moved to areas where close relatives would cause cross-breeding.
