A stronghold of Desmoulin's Whorl Snail, an endangered species protected under British and European conservation laws, has been discovered in the path of the pounds 100m road at the Rack Marsh Nature reserve.
The Government is committed to ensuring a "favourable conservation status" for the snail but the Newbury bypass will slice through the reserve on a 100m-wide embankment.
Under an EU directive the Government is obliged to establish a Special Area of Conservation (SAC) for the mollusc.
Environmentalists are calling for the immediate establishment of an SAC to protect the snail. Caroline Steel, head of conservation for the Wildlife Trusts, said: "This road could be a disaster. It could contribute to the extinction of this species."
The Highways Agency said they were not considering delaying construction of the road to allow the snail's habitat to be protected.