Dogs used to find hedgehogs on the Hebrides now wear muzzles after two hedgehogs died, according to a Scottish Natural Heritage (SNH) report.
SNH has been trapping hedgehogs because they eat the eggs of wading birds, whose numbers are in decline.
The two deaths were believed to be linked to dogs picking up the animals.
A report to SNH's board said hedgehog welfare was taken seriously, but its authors warned deaths could risk future funding to the project.
The public agency has been leading the Uist Wader Project, which sees hedgehogs trapped and then relocated to mainland Scotland.
Over the last seven years, about 1,500 animals have been removed from North Uist and Benbecula.
Hedgehogs are not native to the Western Isles.
Sniffer dogs and their handlers search for evidence hedgehogs' habitats and also the animals themselves.
The report said the introduction of dogs to the project had resulted in a "significant improvement in the efficiency of hedgehog location and removal".
The hedgehog deaths were discussed with animal welfare organisations, including the Scottish SPCA.
One animal died of injuries after being picked up and the other was suspected of dying in similar circumstances.
According to the report, the use of muzzles had not affected the dogs' ability to seek out hedgehogs.
But its authors warned: "Risks relate to the availability of funding and the risk to SNH's reputation if we are not considered to be paying sufficient regard to hedgehog welfare issues.
"Although there are welfare concerns associated with the use of dogs, mitigation measures outlined are acceptable to welfare organisations and through discussion with these organisations, development of clear protocols is ongoing."
SNH said the project adhered to extremely high welfare standards.
A spokesman said: "Welfare is at the heart of what we do - that is why the Uist Wader Project has the Scottish government, the Scottish SPCA, Western Isles Council, and Uist Hedgehog Rescue, along with SNH, as advisors and partners."
He added: "The use of sniffer dogs allows us to locate hedgehogs in difficult terrain and much more quickly than previously.
"Support has been given for the continued use of the dog while wearing a muzzle. The dog has successfully located hedgehogs while wearing the muzzle and no further injuries to located hedgehogs have occurred."
The same report to SNH's board said there was no statistical evidence at this stage that removing hedgehogs had led to an improvement in populations of wader birds.
However, it said understanding the causes behind the fall in bird populations was difficult.
SNH said further planned research was expected to demonstrate the benefits of removing hedgehogs.