They say that during the recent operation - one of the biggest horse culls carried out in Australia - some animals were merely wounded and were left to die lingering, painful deaths.
Brumbies are the descendants of horses that were released into the wild from the 1830s onwards, or which escaped from rural properties.
They spread across the continent, where nowadays their numbers are estimated at anything between 300,000 and one million - believed to be the world's largest wild horse population.
To some, they are a unique part of the nation's settler heritage, and indelibly linked to the romance and adventure of the Outback, particularly in the national parks of the Australian Alps - the "high country" of Victoria, NSW and the Australian Capital Territory.
Conservationists, however, say they are trashing the delicate alpine environment, with its fields of wildflowers and wetlands containing rare Corroboree frogs.
Other endangered species the horses are said to be threatening include the alpine she-oak skink and alpine tree frog.
With their hooves, heavy weight and herbivorous diet, brumbies damage swamp and grassland habitats, polluting and eroding waterways, spreading weeds and competing with native wildlife for food.
Government surveys suggest their numbers have exploded over the past decade, increasing by 21 per cent a year in New South Wales, Victoria and the ACT.
Traditional management methods involve trapping and rounding up horses, then relocating them to farms or pony clubs, selling them at saleyards or euthanising them. However, advocates of aerial culling say it is cheaper, more efficient and more humane - particularly in the Alps, where the animals have to be tracked over exceedingly rough country.
The RSPCA has criticised the Victorian government, which is developing a new brumby management plan but has already ruled out aerial culling, accusing it of prioritising uninformed public opinion over animal welfare.
The organisation believes that if numbers are not reduced, many horses will die because of insufficient food and water.
The RSPCA's president, Lynne Bradshaw, told ABC radio that although the notion of a cull was always "unpalatable", animal welfare experts had "honestly looked at all the options, and this was the most humane method".
In aerial culls, each animal is shot more than once to ensure it is dead. However, the vet who oversaw the operation in the Kimberley, Jordan Hampton, has admitted that 1 per cent of brumbies were not killed properly, and risked "having ... a protracted death".
Libby Lovegrove, spokesperson for Wild Horses Kimberley, believes that brumbies should be managed through a sterilisation programme. She described culling as "a barbaric act of cruelty" and a "shocking, murderous situation".
