While the discussion stemmed from one housing application, members say there is a much bigger problem with how local decisions are handled at a national level.
North planning chairman Drew Millar called on the leader of the Highland Council to open talks with the Scottish Government.
The controversy began with a simple housing application in Kyleakin, Skye as reported in last week's Lochaber Times.
Caroline Clouston applied to build a new home in an area of land she owns beside her current property but SEPA objected to the plan, stating the plot lies within an area at risk of 1-in-200-year flooding.
However, north planning committee took a different view. Deciding the case last August, councillors said the area has never flooded in living memory. Skye members warned that refusing planning permission could set a precedent that would hamper development along the Highland coast.
The committee voted to grant permission.
Because SEPA is a national agency the case then had to go before Scottish ministers who overturned the council’s decision.
Last week's north planning committee formally discussed the application and they did not hold back.
The new SNP chairman Drew Millar told members that he was disappointed with the decision of the Scottish Reporter.
He also said the SEPA's approach was inconsistent, because it does not object to home extensions but does object to new builds.
In response, planning manager Dafydd Jones said a new home would potentially increase the population of the flood-risk area.
However, councillor Millar said the judgement had serious implications for Skye and the entire West Coast.
Skye councillor Ruraidh Stewart claimed the Scottish Government has overturned around 60 per cent of Highland Council’s north planning committee decisions.
Former north planning chairwoman Maxine Smith lobbied on this issue during her time at the helm.
'We’ve got the ear of people and we know the local area, then Scottish ministers come along and overturn it,' she said, urging constituents to highlight cases like these in the press and keep lobbying their MSPs.
Mr Jones reminded members that the key issue in this case was flooding. 'When the impacts are felt they will be very real,' he said.
Chairman Mr Millar said he has asked council leader Raymond Bremner to open discussions with the Scottish Government.
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