The warning comes as a study will examine possible sites where animals injured by turbines could end up stranding.
The new University of the Highlands and Islands is offering a postgraduate studentship in the research.
UHI said how the animals would behave around turbines was unknown.
The development of marine renewables in Scotland is still in the early stages with prototype devices being built and tested.
A report published in 2010 on the potential benefits of harnessing wave and tidal power suggested £2.5bn could be spent in Scotland and 5,300 jobs created by 2020.
Industry forum Scottish Renewables and development agency Scottish Enterprise had commissioned the study.
Scotland’s waters provide habitat for dolphins and killer whales as well as large fish such as basking sharks.
A study of harbour porpoises suggested one turbine could come into contact with up to 13 animals in one year, according UHI’s information on the studentship.
However, the university added that the number of collisions in reality was expected to be much lower.
The new research will investigate where injured animals and the bodies of dead ones could potentially end up.
It will look at how carcasses are carried on tidal current and moved by wind and waves onto beaches.
Oban’s Scottish Association for Marine Science, which is part of UHI’s network of colleges and research centres, will host the study.
UHI said: “For the species at risk, collisions could have welfare and population consequences, for regulatory agencies they may have conservation implications and for developers and utilities they run the risk of damaging the devices, imposing uneconomic consenting requirements and alienating public opinion.
“Consequently establishing a good understanding of the magnitude of this potential show-stopper is important to the efficient growth of this Scottish-led energy sector.”