Energy industry regulator Ofgem has been reviewing transmission fees paid by generators to connect to the national grid.
But Mr Ewing said yesterday that the proposals could see power generators in the Western Isles paying 77 times the fees of those in south-west England.
He raised fears of the impact this would have on renewables projects in the islands, adding it was in such areas that green energy was “most abundant”.
He spoke out on the issue in a debate at Holyrood, telling MSPs: “Charging for access to the electricity transmission network remains absolutely central to the future of electricity generation in Scotland. What is at stake is the future development of renewable energy in the western and northern islands.
“We find ourselves poised to exploit some of the most outstanding wind, wave and tidal energy resources in the world. But we cannot do that with a system which deters investment.”
Mr Ewing said it was “highly disappointing” that Ofgem’s proposals would “continue to discriminate against the islands, and do so to a marked and grotesque degree”.
He added: “They would see charges of £1 per kilowatt for connection to the grid for developers in the south-west of England, but they would charge £60, £67 and £77 per kilowatt for connection to Orkney, Shetland and Western Isles respectively.”
Mr Ewing acknowledged Ofgem’s reforms were “not all bad” – costs for mainland generators would fall from £28 per kilowatt to less than £10.
Labour’s Ken Macintosh agreed that the Scottish Parliament should “unite in sending a strong message to the electricity regulator Ofgem on transmission charges, to treat Scotland and its islands fairly”.