Government scientists will recommend that part of the route of the pounds 101m road should be designated a European nature reserve - because of the rare and tiny Desmoulin's whorl snail.
If English Nature's ruling council accepts its scientists' view, then the Government will face serious legal challenges in proceeding with the bypass.
The scientists from English Nature, the Government's wildlife conservation arm, are understood to say the dual carriageway road will cover two of Britain's best riverside sites for the snail. They are recommending the land should be designated as Special Areas of Conservation (SACs) under the European Union Habitats Directive.
Lawyers acting for three nation-wide conservation organisations will be seeking an opportunity to take legal action, in Britain and in the European Court, over the snail versus the road. Friends of the Earth said it would try to find ways of getting an injunction halting the main construction work, due to start in less than four months.
The snail and its haunts are covered by the Habitats Directive because it is an "indicator species" for chalkland fens - a marker for a rare and declining European habitat.
It is already on a list of 116 threatened British plant and animal species for which the Government is considering rescue plans. Today, the Secretary of State for the Environment, John Gummer, is due to publish his conclusions on the list of 116.
Among the whorl snail's British strongholds are the valleys of the Kennet and Lambourn. The eight-mile bypass will cross these chalk streams on large earth embankments.
If English Nature's council does go along with its scientists' recommendations, then the Government could still drop the Newbury bypass sites from its final version of the list of snail SACs.
If it did, Friends of the Earth, the World Wide Fund for Nature and the Wildlife Trusts would consider seeking a judicial review.
Alternatively, ministers could accept the bypass SACs - but then argue that the road still had to be built on the grounds of overriding economic importance.
But to comply with the directive the Government would have to review the bypass, show that there was no alternative which missed the snail sites and offer a mitigation package, including alternative protected areas.
Ministers would have to delay construction work while they went through that review process.
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