Animal rights campaigners have called on the Scottish Executive not to introduce legislation which would give it wider powers over slaughter.
Ministers are being urged to use measures other than slaughter
The Duchess of Hamilton, on behalf of Advocates for Animals, has handed in a report and urged ministers to use other methods to deal with disease outbreaks.
Campaigners fear the new animal health bill would allow culling without full explanation and justification.
However, the executive said decisions would be based on scientific advice.
A spokeswoman said the measures included options for vaccination.
The Advocates for Animals report, "The Control of Transmissable Animal Diseases", includes analysis of scientific literature and latest developments on disease control methods.
Under the existing Animal Health Act 1981, the executive already has powers to slaughter animals that are infected with certain diseases, have been in contact with infected animals or have been exposed in any way to disease.
The animal campaigners are concerned that the new bill, the Animal Health and Welfare (Scotland) Bill, would also give ministers the authority to slaughter animals in sanctuaries and pets such as birds, cats and dogs.
Advocates for Animals said the wording used in the bill was so broad that it would make it almost impossible for a challenge in the courts.
The group said it was now widely accepted that emergency "ring" vaccination, rather than mass killing, should play a leading role in any future infectious disease outbreaks.
The executive said animal vaccination was an option
Advocates for Animals director Ross Minett said: "Whilst we welcome much of what is contained in the new bill, we believe that the proposed unlimited slaughter power is not a proportionate, scientific or humane response to the problem of future animal disease outbreaks.
"As our report shows, instead of introducing draconian mass slaughter powers, the Scottish Executive should be stepping up its efforts to ensure that effective vaccination and testing regimes are in place."
The Environment and Rural Development Committee began taking evidence on the proposed bill on Wednesday.
Deputy convener and Green MSP Mark Ruskell said: "I have significant concerns that the powers proposed in this new legislation are too wide.
"In effect, ministers could order the culling of thousands of animals without having to give any explanation.
He added: "We must do whatever we can to avoid a repetition of the terrible scenes of devastation that the UK witnessed in 2001 during the foot-and-mouth crisis.
"Vaccination is now the norm - the science supports this position. Culling should only be consider as an absolute last resort and it should be fully explained and justified."
A Scottish Executive spokeswoman said: "The bill proposes maximising our flexibility to eradicate a wide range of animal diseases quickly and effectively to minimise suffering.
"Use of the proposed new powers to slaughter would not be automatic.
"They are part of a suite of measures, which also includes powers to vaccinate, in which decisions would be made on the basis of scientific and veterinary advice."