More than 6,000 wild buffalo, horses, donkeys and pigs have been culled from the Kakadu National Park under a feral animal eradication program.

The dead animal count includes 3,652 wild horses, 1,965 buffalo and 294 pigs, all shot from a helicopter over mostly inaccessible areas.

The World Heritage-listed park, two hours east of Darwin in the Northern Territory, is famous for its vast wetlands and native fauna and flora.

Manager Pete Cotsell said the 24-day operation focussed on key areas in the Mary River region.

"Probably in the more sensitive areas of the park such as the sandstone country where there are pristine springs, they're doing a lot of damage," he said.

"Six-thousand animals is equivalent to 24,000 harsh hoofs which are around waterways, digging up the mud and sending plumes out into these sort of pristine wetland areas.

"So they are doing a significant amount of damage and the spread of weeds as well is a big issue."

Mr Cotsell said they worked with three local Aboriginal communities to ensure rangers were not shooting animals that locals wanted to hunt.

"We undertook some really extensive consultation across the park because we're well aware that some of these animals have more meaning to the traditional owners," he said.

The animal count includes 3,652 wild horses, 1,965 buffalo and 294 pigs, all shot from a helicopter. ( Supplied: Parks Australia )

"Together we drew some boundaries around maps … [and] we took some meat out to the communities as well."

In recent years, the price for wild buffalo has risen significantly, driven largely by the live export trade with Vietnam.

Mr Cotsell said aerial mustering was being considered in the future to take advantage of the demand presented by overseas markets and the Darwin abattoir.

"We're also working with the pet-meaters along the highway to explore opportunities for pet-meating as well," he said.

"What we've done this time is do the cull well away from highways where the animals aren't accessible.

"So really we've been focussed on those areas where the animals have no economic value whatsoever and later on during the year we'll look at opportunities along the highway."