Islanders are angry that ministers announced a 10% fare increase for lorries on ferries without waiting for the results of research they commissioned.
The study commissioned by the Scottish Government, which was due to be published next month, found the decision to remove the Road Equivalent Tariff (RET) cheap ferry fare scheme from commercial vehicles is hitting the most fragile island communities hardest.
It also found the benefits of RET were largely passed on by hauliers to local businesses. However, one of the arguments used for withdrawing RET from the commercial vehicles was that the RET savings of up to 50% were not being passed on by hauliers.
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It was announced in September the MVA Consultancy would assess the withdrawal of RET.
MVA got responses from 49 businesses affected, with the study concluding that the more remote communities are likely to face greatest impact. But it says removal of RET is having a negative impact across all islands affected.
A spokeswoman for Transport Scotland said: "We intend to consider the findings of this study first, then set up a working group to take this forward, consulting with key stakeholders as we do this."
She said £2m was being spent to limit the increase to 10%. "This is a significant reduction to the average 34% increase planned for 2013 under the transitional arrangements."