Deer in Gloucestershire and on Exmoor could be under threat from tuberculosis spread by badgers and cattle.
Deer are at risk but the source of TB may not be known until 2006
The warning has come from government vets who say the number of undetected cases in the animals could be higher than previously thought.
Some farmers want a cull of badgers but the Department for Environment, Food and Rural Affairs (Defra) says there is not enough evidence to back the move.
It is carrying out surveys to trace the cause of the disease.
The trials are being held in rural areas across the West of England, including Gloucestershire and the Somerset/Devon borders.
They started in 1999, but were delayed by the foot-and-mouth outbreak in 2001.
The trials are due to finish next year and the results are expected to be published in 2006.
"There are reservoirs (of TB) out there," a Defra spokeswoman said.
"But we are waiting for science to tell us where there are and how we sort them out."