The Herald revealed that Caledonian Maritume Assets Ltd, the public body which owns the majority of Scotland's vessels and ferry infrastructure, is preparing to apply for EU funding for the project after an initial feasibility study - part funded by £200,000 from Scottish Enterprise - indicated that the technology was "not impossible".
The vessel would be powered by a hydrogen fuel cell which could be recharged while it docked in harbours overnight using surplus wind and tidal electricity generated on the islands.
However, Scientific Alliance Scotland accused the Scottish Government and Scottish Enterprise of wasting taxpayers' money for wasting £200,000 of taxpayers' money on the three-year study.
Professor Jack Ponton, of SAS, said the technology was risky.
He said: "Hydrogen is just about the worst energy carrier one could imagine particularly as a transport fuel. It is difficult to store or distribute and poses serious explosion risks. It is in principle a valuable chemical feedstock, but industry is not geared up to use it in large quantities."
CMAL is seeking innovative ways of cutting emissions, having already invested in three hybrid ferries.
But Prof Ponton added: "Carbon dioxide emissions from island ferries are a negligible part of Scotland's emissions, which are themselves trivial on a global scale. In other words, this scheme is just a silly idea to use up the taxpayers' money."
The Scientific Alliance was established in 2001 as a forum for scientists and non-scientists to debate and discuss environmental issues.
It has published a number of papers criticising the push towards renewables, particularly wind energy, and has taken a relatively sceptical approach to mainstream claims on climate change.
Its director, Martin Livermore, previously criticised attempts to "shut down" the debate and has suggested that heightened solar activity may be the real driving force behind the greenhouse effect.
Andy Crossan, Senior Technical Manager, CMAL said: "There is growing cross-sector support for the potential use of hydrogen in a marine environment. We're exploring the options to make hydrogen fuel a reality in a marine application as can be seen in the applications currently being used effectively for cars and buses both in Europe and North America.
"So far, our work has found no technical reason why we cannot achieve this goal, but we are well aware that there are a number of phases that still have to be conducted to reach a blueprint for a viable sea going ferry application.
"Maritime safety and security is stringent and the use of hydrogen fuel in a marine environment will be equally robust."