Labour MSP Elaine Murray said she was disappointed that the Scottish government's draft
did not include a new Lochboisdale to Mallaig ferry service, on 22 March 2012.
Ms Murray said there had been no vehicular service on this route for over ten years and there was huge support in the Western Isles and Mallaig for it.
The draft plan is in the consultation process at the moment and closes at the end of this month.
The Dumfries MSP said it would have many benefits for the local economy, tourism and carbon reduction.
She also commended the campaigning of the Lochboisdale to Mallaig ferry group who called the absence of a service "the missing link" and said she hoped one of the government ministers would meet with the group.
Infrastructure Secretary Alex Neil said based on a 2005 report a new vessel would cost about £26m and around £3.5m to £4m per annum to run and that the onus was on the Labour party to tell the government where would the money come from.
Mr Neil said: "Elaine Murray has to tell us, if she is going to be honest, she has to tell us where the money is going to come from."
"Does she want the £26m spent on the new ferry from Lochboisdale to Mallaig instead of the upgrade of the A75 that she said should be a top priority for transport in Scotland?"
He also said the government were listening "very very carefully" to what the campaigners from South Uist were saying and they would engage with them after the consultation period had ended about the pros and cons of the service.
Conservative MSP Mary Scanlon said there was no doubt that a new Lochboisdale to Mallaig was a very popular option for people in Uist.
Ms Scanlon said the new service would be good for business and tourism and would alleviate traffic and reduce travel times.
Liberal Democrat MSP Jim Hume said that a new Lochboisdale to Mallaig ferry service not being included in the draft plan was a "hammer blow to lobbyists".