A little more than two weeks ago, Mark Lintermans headed into the high country to give some fish electric shocks and save them from extinction.

The fish in question was the stocky galaxias (Galaxias tantangara), an endemic freshwater species that grows to about 10cm and is known to live wild only in a three-kilometre stretch of Tantangara Creek, in the Kosciuszko national park.

Scientists estimate there may have been a couple of thousand stocky galaxias remaining before this summer’s bushfires. As with many species, they are now unsure how many are left.

The species is considered critically endangered by the International Union for Conservation of Nature (IUCN), but it is not listed as threatened in Australia because it has not been formally assessed.

In the absence of the monitoring or funding that can come with a national threatened species listing, Lintermans, a freshwater scientist at the University of Canberra, and the NSW Department of Primary Industries organised a rescue mission on 15 January.

He says it was unclear at the time if fire had affected the species, but a forecast downpour would have.

“Fish will survive the initial fire pretty well, but what they can’t survive is rain that washes ash into the water and turns it into liquid Vegemite,” Lintermans says. “It smothers the fish, smothers their gills, smothers their food source and smothers their breeding habitat.”

The only known home of the stocky galaxias is a 3km stretch of creek in Kosciuszko national park. Photograph: Chris Walsh of NSW DPI

The effect of the ash is compounded by dead leaves washing into waterways. As organic matter decomposes it draws oxygen from the water, potentially triggering mass fish kills. Ash and decomposing material have contributed to the death of thousands of native fish at more than 20 different locations across the Murray-Darling Basin and in coastal areas of NSW over the past fortnight.

At Tantangara Creek, Lintermans’ team used a technique known as backpack electro-fishing. The scientists introduce a direct current into the stream, stunning the fish enough to cause them to stop swimming, roll over and expose their light-coloured underbellies, making them simple to catch with a small net. Once free from the current in a water-filled bucket they usually recover within seconds.

The trip to Tantangara was a success. Lintermans led the rescue of 142 stocky galaxias and transferred them to a temperature-controlled hatchery. He would have preferred to collect 500 to give the species the best chance to ensure a genetically diverse population in captivity, but about 150 is considered enough to offer hope.

A second trip last week to rescue another galaxiid species, the short-tailed galaxias, was less successful. The short-tailed variety lives near Numeralla, north-east of Cooma, in two waterways separated by a stream infested with predator trout. One population was in an area too dangerous to visit due to fire. The other was badly affected by drought, its home reduced to a series of muddy puddles. Only about 30 fish could be recovered.

‘You can lose a species. I don’t want that on my head’

Lintermans fears for the future of both species. He says the stress of his scientific work is even greater than what he felt when serving as a volunteer firefighter in his youth.

“If you don’t get it right, if you don’t get in soon enough, you can lose a species. I don’t want that on my head,” he says. “Some of these things I’ve been working on for 35 years so it’s part of my family, you know.”

The two galaxiids are among an unknown number of species that scientists say are yet to receive much attention in the wake of the bushfire crisis, but will need it. The federal government has been quietly praised by experts for its initial response to the wildlife emergency, including the quick release of an analysis that mapped how much of the known habitat of 331 nationally listed threatened and migratory species had burned.

Scientists at the site of the fish rescue, Tantangara Creek. Photograph: Supplied by Assoc Prof Mark Lintermans

But experts are also concerned for species not on that list. While the plight of the koala and platypus were quickly highlighted, fish, frogs, reptiles, insects and other invertebrates have received less attention.

Of 89 Australian freshwater fish species listed as globally threatened by the IUCN, only 38 are recognised under national environment laws as at risk and requiring protection. It is estimated about a quarter of freshwater fish species are yet to be described.

Lintermans says the stocky galaxias clearly warrants formal protection, which would bring it some funding for monitoring and further research into its distribution and the threats it faces.

“I actually nominated it to the federal government quite some time ago, it just hasn’t got out the other end of the sausage machine yet,” he says.

“The neglect of the fish side of things has really put us behind the eight-ball in terms of rescuing them or monitoring them. I’ve been banging very hard against that door for five years now and haven’t made any headway.”

He says part of the reason for the slow progress has been the shift to a single operational list for threatened species, under which state lists are being reassessed at national level. Environmentalists also point to deep cuts in funding for environmental protection since the Coalition took power in 2013.

Lintermans says the government is doing what it can to respond to the fires under adverse conditions, including asking leading scientists for advice on recovery strategies at roundtable events. He attended one hosted by the environment minister, Sussan Ley, last week. But he says the test will be whether the initial $50m in funding for the wildlife response is followed with what is needed in the long-term.

Several scientists who attended last week’s round table say discussion focused on the need to improve monitoring of species, echoing a point earlier raised with Guardian Australia by Helene Marsh, the chair of the government’s threatened species scientific committee.

David Lindenmayer, a professor at ANU’s Fenner School of Environment and Society, says there is little hope of learning anything about the impact of fires on threatened species without better data collection. “Almost everyone around the table agreed we can’t help the way we want to help unless we get the long-term monitoring in place,” he says.

Lintermans stresses the focus of that work needs to be broader than just mammals, birds and plants, as important as they are. “The real critical bit is whether enough funding is going to go to species that need long-term help,” he says. “Are we going to just get distracted again by the charismatic species?”