The Lisnaragh site near Strabane was declared an area of special scientific interest (ASSI) in March. But Wilson rescinded the Council for Nature Conservation and the Countryside's advice, even though it is a statutory adviser to his department. The Environment Agency backed the safeguards.
Friends of the Earth campaigner Lisa Fagan said: "Wilson's U-turn raises key questions. Has he overturned official advice to clear the way for mineral exploitation of an Ice Age site? Will he fulfil his statutory duty to protect it or leave himself exposed to legal challenge?"
An Environment Agency report issued in September says several objections to the ASSI designation came from landowners who think that it will restrict the potential for exploiting sand and gravel deposits on their lands.