The Western Isles Council has voted to reduce the subsidy to the service that links Stornoway on Lewis with Benbecula and Barra.
The Barra leg will definitely be axed, saving the council £168,000 a year. However, plans to cut the Benbecula-to-Stornoway leg from five to three days a week, which would save £173,000, have been deferred, pending another approach to NHS Western Isles for a contribution as a frequent user. If the request for funds is refused the cut will go ahead.
The petition will be lodged with the Scottish Parliament's Petitions Committee with the aim of it being discussed by the committee when it visits Stornoway next month.
Angus MacNeil, the islands' SNP MP, said the petition was being launched to save a vital service. He said: "I would urge everyone who can to sign this petition, which will shortly be available online and in local shops throughout the Hebrides over the coming days.
"If implemented, these cuts will severely undermine the current inter-island connections, and will set back the transport connections that have been so important in connecting the north and south in the Hebrides over the past 40 years.
Western Isles MSP Alasdair Allan said: "I know how vital this service is to linking the islands."
But Angus Campbell, the council leader, said the authority was having to cut the Barra service subsidy because of the requirement for local government cutbacks.
He said that, due to local authority funding being frozen, the council had to find the equivalent of the cost of inflation – £3.2 million over two years.
It is also faced with a grant reduction from the Scottish Government of £2.1m by 2014/15, and he said these factors made up the bulk of a budget shortfall of £5.5m.
He added: "Angus Macneil and MSP Alasdair Allan have both said the Comhairle (council) should continue to fund the Barra/Benbecula service, which is mainly used for local authority, health board and tourism purposes.
"However, a recent study showed that in 2011 one-third of passengers were sightseers, 14% were NHS employees and 4% were council staff. The subsidy per passenger per one-way trip is £83. Three-quarters of seats are flown empty. Passenger numbers on the Sound of Barra ferry are more than 20 times those on the air service."