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The letter has annoyed protesters including Scottish Socialist Party environment spokesperson, Glasgow MSP Rosie Kane.
She claimed it was an implied insult to objectors by suggesting they were wrong and had no need to raise their concerns.
A spokesman for protest group, TRANSform Scotland, claimed it showed the Executive was desperate "to bulldoze this motorway through" and suggested it could be looked on as an attempt to frighten people off.
Green Party spokesman Chris Ballance said the inquiry had "an air of sham about it all".