The road equivalent tarriff (RET) scheme, being trialled in the Western Isles, could spread to ferries in the rest of Scotland.
Fares could be made substantially cheaper under the scheme, which links prices to the cost of travelling the same distance by car.
Transport Minister Keith Brown said the RET scheme "underpins the way forward for ferry fares".
Last month the Scottish Government said RET would become standard in the Western Isles, Coll and Tiree.
Under the draft Ferries Plan the scheme will now be tested for passengers and cars, including small commercial vehicles, across Argyll and Clyde islands in stages across this five-year parliamentary session.
The report, published on Wednesday, said the current fares system was "unnecessarily complicated and no longer fit for purpose".
It added: "The current system of fare-setting is not transparent or easily understood by people who use and rely on their ferry service."
It proposes replacing the current route-specific system for fares setting with one system, making RET the basis for single fares for passengers and cars.
Mr Brown said: "We want to build on the momentum generated by our recent announcement to extend the RET during the lifetime of the current parliament, and the draft Ferries Plan provides a raft of further positive proposals.
"We believe the RET underpins the way forward for ferry fares and we plan to replace the current route-specific nature of fare setting with RET as the basis for fares for passengers and cars."
The draft plan also proposes a number of changes to ferry services across Scotland, including upgrading the Ardrossan to Brodick service to Arran to a two vehicle service, with more frequent sailings through to late evening.
Later evening sailings one or two times a week are suggested for Cumbrae, while the plan also proposes increasing sailings to Barra in the winter and improving the winter service between Coll and Tiree.
With many of Scotland's ferry services funded by subsidies from the Scottish Government and local authorities, the plan said that public money should be targeted to support services which "are essential to the community".
Information from Tony Wilson
