The move comes after about 10,000 of the species have made their home over the years in North and South Uist and Benbecula.
Crofters' representatives have long been demanding a change in the law so greylags, the bulkiest of the wild geese native to the UK and Europe, can be shot throughout the year and their meat sold.
Scottish Natural Heritage (SNH) has now announced help is on hand for farmers and crofters in the islands, in the form of a pilot scheme that will introduce their shooting and sale locally under licence.
There is a general prohibition of the sale of wild goose carcasses. It was introduced in the 1960s across the UK for conservation reasons to remove any commercial incentive in relation to hunting geese. But wild goose carcasses can still be consumed or given away.
However, this is the first time SNH has licensed the sale of goose meat in Scotland under the Wildlife And Countryside Act 1981. The scheme is also being trialled in Orkney.
SNH says the long-term goal is to minimise agricultural damage while maintaining a viable goose population.
Selling geese shot as part of this management will help generate important income for the community and help pay for some of the work.
Licences will initially be provided to enable the sale for a trial period from this month to March 2015.
Environment Minister Paul Wheelhouse said: "I welcome the progress made by crofters and farmers who have been working with SNH to manage populations of resident greylag geese to prevent serious agricultural damage.
"These carefully controlled licences will allow the local sale of fresh wild goose meat and so prevent the waste of a resource and provide an economic opportunity for the community."
Johanne Ferguson, SNH's operations manager for the Outer Hebrides and secretary to the local goose group, said: "This is an exciting development. Several local businesses are interested in developing goose products while others are looking forward to using and promoting delicious local wild goose on their menus."
The community-led Storas Uibhist, which owns 93,000 acres covering almost the whole of the islands of Benbecula, Eriskay and South Uist, hold the licences for these islands.
Chief executive Huw Francis said: "This can only help the crofters protect their land from the impact of the geese on their grazings and crops."
RSPB Scotland is also supportive