The Scottish Parliament has been hearing an appeal from conservationists who want to protect the hedgehogs.
The board of Scottish Natural Heritage (SNH) sanctioned the slaughter in an effort to help preserve rare birds on the Uist isles.
The hedgehogs are due to be killed by lethal injection in a few weeks time.
Members of the British Hedgehog Preservation Society (BHPS) appeared before the parliament's petitions committee in Edinburgh on Tuesday.
The hedgehogs are accused of eating the eggs of rare waders during the breeding season, causing a drop in the waders' numbers.
The conservationists want the chance to collect and move the hedgehogs to new homes on the mainland before extermination begins.
SNH told the committee it was prepared to seek ways of saving some of the animals but insisted the society's proposals were not based on robust evidence.
SNH deputy chairman Michael Scott ruled out delaying the cull, but said only 200 of the animals were expected to be caught this year.
He said SNH was due to meet BHPS and other animal welfare groups next week in a bid to find a way forward on the issue.
However, he said the expert advice to SNH to date was that transportation was likely to cause "most suffering to the animals".
Relocation
The society's Kay Bullen told BBC News: "We're suggesting instead of culling them, taking them off the island and putting them on mainland Britain.
"We believe this can be done without having a detrimental effect on either the hedgehogs being relocated or the mainland population."
She said such a mass hedgehog relocation had not been done before, but hedgehogs were regularly taken in from the wild, nursed and released.
A handful of hedgehogs were first introduced to the Uists in 1974 to help control slugs and snails in islanders' gardens.