Several species of rarely sighted birds lived in the 500 hectares of the Waituna Wetlands Scientific Reserve destroyed by fire, with some of the birds nesting at the time of the blaze, experts say.
The Awarua Wetlands, near Invercargill, is one of the largest remaining wetlands and is recognised for its biological diversity, cultural values and bird life.
Conservation Department Southern Islands area manager Andy Roberts, who is also the Southern Rural Fire District's incident controller, said bird species in the manuka bush and wetlands in the Awarua Bay area included bitterns, fernbirds and crakes.
Birds were nesting in the area but it was unknown how many were lost.
Southland Fish & Game manager Maurice Rodway said other birds that would have been affected by the fire included grey warblers, harriers and fantails.
The cause of the fire, which was under control last night, remains unknown.
Southern Rural Fire Authority spokeswoman Sally Chesterfield said fire investigators had been at the scene but the cause of the blaze, which has been battled by fire crews since Monday night, had not been determined.
A strong northwesterly wind fanned the fire as it raged, and difficult terrain caused problems for firefighters.
Fortunately, the area was not too dry, so the fire was burning only on the surface and not underground, she said.
"With the water levels the way they are, [the fire] can't burn down into the peat. If it was deep in the peat, we'd have a much longer-term fire on our hands."
Terrain was very wet underfoot, and it was difficult to get heavy machinery into the area, she said.
GPS co-ordinates taken by one of the helicopters above the site showed the fire was in an area of 499 hectares, with vegetation mainly manuka and low coastal scrub.
Staff from the rural fire authority, Invercargill City Council and DOC were joined by helicopter crews, carrying monsoon buckets of about 1200 litres of water from the nearby Awarua Bay to douse the flames, and an incident command centre manned by two members of the Invercargill fire brigade.
Teams will patrol the fire perimeter again today, dampening down hotspots and ensuring the fire is out.
The fire swept through conservation estate but had not threatened homes or property.
The only loss was a long-drop toilet, at one of about 25 huts in the wetlands.
Authority principal rural fire officer Mike Grant said although there had been wet weather in Southland, with average rainfall recorded, areas that had scrubby vegetation dried out extremely quickly after rain and could burn within two to three hours, even in the cold.
Farmers Derek and Jolene Ballantine said they were able to see thick smoke billowing and flames "exploding" from the kitchen window of their Marshall Rd property on Monday night.
Emergency services were alerted to the fire about 6pm on Monday by a member of the public.
Yesterday, the Ballantines were among a handful of people gathered at the edge of the Waituna Lagoon, keeping a close eye on the fire's progress.
Ballantine said they had seen the fire spread all the way from Awarua Bay, near Tiwai Pt, all the way down to the edge of the lagoon, before it was forced to split at the water's edge.
"Within 20 minutes, you could just see it spread."
Mrs Ballantine said: "You can see how much of a hard task it's been for them trying to keep that under control . . . We're about three or four farms back, really, so that's a lot of flames to be glowing in your kitchen window.
"It's a bit unsettling - you know you're safe but it's still that primal thing isn't it, you think 'I shouldn't be this close to a fire'."