Economist professor Neil Kay called on transport minister Keith Brown to dissolve the group and replace it with a panel of independent experts.
In a resignation letter, Professor Kay criticised the group for secrecy and closed-door meetings and said the interests of service-users and communities were "peripheral".
He said: "It is now clear that the structure and working practices of the group are designed to voice and promote producer interests, including that of (some) established operators.
"The interests of those users and communities dependent on those ferry services are and will be peripheral in such a forum when they should be central … it would be better described as a platform for lobbying."
The Scottish Government created the expert ferry group (EFG) last year to advise ministers. The panel, which includes chief executive of SPT, Gordon Maclennan, and Brian Fulton, operations director for CalMac, met for the first time in October.
Professor Alf Baird, a member of the panel and an academic at Edinburgh Napier's Transport Research Institute, said he regretted Professor Kay's resignation but did not share his views.
Professor Baird said: "There are only two operators [CalMac and Western Ferries] on the EFG, therefore I don't believe it can be said to be dominated by operators. A large proportion of the group are actually from public bodies, who in turn represent users."
A spokesman for Transport Scotland said it was "very disappointed" by Professor Kay's departure. He said: "We have been clear from the start of this process that all discussions and advice relating to the EFG would be private to allow the group to have frank and open discussions on the future of the ferries sector. We believe interest of ferry users is central to the group's work."
He said agendas and minutes of EFG meetings would be published on Transport Scotland's website.