The research is into the feasibility of a Gourock-to-Dunoon car ferry service on which only the passengers are subsidised.
It is in response to more than a year of complaints in Dunoon and Cowal about the passenger-only service introduced last year by Argyll Ferries, a sister company of publicly owned CalMac.
Passengers are still angry that in 2011 Government agency Transport Scotland ended CalMac's vehicle-and-passenger service, and the SNP failed to build two new ferries for the route, as promised in opposition.
Tory Highlands and Islands MSP Jamie McGrigor questioned whether the study was justified by Argyll Ferries' poor performance. Official figures show only a 0.3% difference between the level of cancelled sailings due to adverse weather on the Gourock-Dunoon route and the nearby Wemyss Bay-Rothesay route run by CalMac.
He said the Scottish Government was already aware performance was in line with other routes. He added "The genuine motives for commissioning this study have to be explained.
"Many of my constituents believe the political desire to see an improved service is undermined by the tender issued by Transport Scotland in 2011 and in light of this new information many would therefore conclude the Government is wasting public money to spin out this issue."
Western Ferries now has a monopoly of vehicle traffic to Cowal. Managing director Gordon Ross said: "The actual performance of Argyll Ferries' service undermines the - need for this study. The Scottish Government are - squandering public money solely for political convenience. This study is - a pointless and cynical move.
"As Western Ferries already operates a highly reliable car ferry service, why commission a study for a competing vehicle service, that if introduced will cost the taxpayer millions and will undermine a successful Dunoon company?"
The cancellation figures, have been disputed by some residents, who say they show the Rothesay service had twice the number of cancellation-free months as the Gourock-to-Dunoon.
There have been decades of debate over CalMac getting a subsidy for passengers travelling on a car ferry, while private-sector Western Ferries got none.
Once in power, ministers claimed the European Commission would not let them build new vessels. But the Scottish Government's claims over European intransigence have been vociferously challenged locally.
A Transport Scotland spokesman said: "The focus of the study is not about the reliability of the services currently being delivered, but in response to the community's aspirations for a vehicle ferry service.
"We share the wish of those in the Cowal community who want to see a vehicle carrying service restored to the town-centre route, but the European Commission has made clear subsidising the carrying of vehicles on this route would be against state aid rules."