THOUSANDS of brumbies will be killed as humanely as possible in western Queensland by a new government squad trained to shoot the horses in the heart and head.

The cull in Carnarvon National Park follows expert advice that Queensland's most fragile ecosystems are under siege from animal pests including horses, camels, pigs, dingoes, deer, rabbits, foxes, cats and even feral cattle, the Courier Mail reports.

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Many thousands have been shot, trapped and baited.

Fears of an outbreak of foot and mouth disease prompted a war on feral pigs, which are also destroying the habitats of endangered birds and marsupials.

Environment Minister Kate Jones said six park rangers using high-powered rifles had been trained to shoot the brumbies in the heart and head for a swift kill.

Similar culls in 2007 and 2008 sparked international outrage from animal rights groups and the Save the Brumby organisation.

Ms Jones said yesterday she could understand animal lovers' concerns. However, the wild horses were causing major damage to the park's fragile ecosystem and shooting them was the most humane way of reducing numbers.

The park could be overrun by up to 45,000 brumbies if action was not taken quickly.

Ms Jones said there would be two, three-day culls.

RSPCA officers would monitor the shoot and a back-up helicopter would be used to dispatch any animal not properly killed by marksmen in the lead helicopter.

More than 6300 horses have been shot in the area since 2007 in one of the world's biggest brumby culls.

An attempt to muster the horses and sell the meat to pet food companies failed.

Ms Jones said there were at least 4450 brumbies in the park. There was no maximum number of horses targeted.

Horses have also been put down north of Mount Isa and west of Townsville.

There are few areas in Queensland free from feral animals, which compete for food with and spread diseases to native animals.

The State Government is spending $4.5 million a year combating pest animals and plants.

At Agnes Water, near Gladstone, wildlife officers warned of a possible outbreak of foot and mouth disease because pigs feed on dead animals washed ashore.

Ms Jones said she was shocked by the devastation she saw in the World Heritage Wet Tropics of north Queensland where pigs and foxes feasted on turtle eggs.

Rampaging pigs were destroying endangered tea tree and feather palm swamps and rainforests. More than 25,000 pigs have been culled there in the last five years.

On Curtis Island, off Gladstone, the Government encourages sporting shooters to cull feral pigs which are destroying the habitat of the endangered yellow chat. Hunters have taken 2084 pigs with ammunition paid for by the state.

Camels causing erosion in the Simpson Desert are being rounded up and stray stock are trampling endangered bilby burrows further west.

Rare plants and the eastern bristle bird and Fleay's barred frog are under assault from feral pigs at Conondale National Park in the Sunshine Coast hinterland.

Between 2002 and 2005, 1200 goats were destroyed on South Percy and St Bees islands.