Scientists are split over the death sentence awaiting Britain's 4,000 introduced North American ruddy ducks.
Environment minister Michael Meacher has decided to allow a cull after considering a report from a specialist task force.
Mr Meacher spoke of "strong scientific evidence" that the ruddy duck poses a serious threat to the survival of the white-headed duck as a distinct species.
Britain has been blamed for being the source of ruddy ducks that migrated to Spain and mated with female white-headed ducks, potentially producing fertile hybrids.
But some scientists are questioning the policy. Christopher Mason, of the University of Essex's biological sciences department and editor of Bird Conservation International, said: "Conservation policy should be based on sound science posted in the reputable journals I and international literature, where people can evaluate it.
"I have been unable to find anything in the Science Citation Index. Is there evidence the birds responsible for interbreeding with white-headed ducks in Spain are British birds? And if the birds are inter-breeding they are by definition not separate species, but sub-species."
Edith Signer of Leicester University, a geneticist who has used genetic fingerprinting studies for the Wildfowl and Wetlands Trust, which underpin the cull, also called for caution.
She said: "The genetic data has to be backed up by observation and ringing recoveries. I am very reluctant to say something based just on genetics."
But Baz Hughes of the WWT said DNA fingerprinting had proved that hybrids remain fertile at least to the third generation.
Chris Harbard of the Royal Society for the Protection of Birds said: "Do you wait for the offchance of one of the small numbers marked to turn up in Spain or do you ask whether there is any way our ruddy ducks could reach Spain.
"It may be deduction but, even if there is no scientific evidence, what seems likely must be the truth. We could wait for 20 years by which time the white-headed duck is likely to be extinct."