Controversial slaughter powers to deal with future animal disease outbreaks have been defended by Deputy Environment Minister Rhona Brankin.
The bill gives ministers more powers to cull animals
Several MSPs and animal welfare groups called for checks to be introduced to a new animal welfare bill.
But proposed amendments seeking formal backing of experts before approving slaughter were rejected by MSPs.
The Scottish Executive had given an assurance experts would be consulted before the extended powers were used.
Opposition MSPs on the environment committee wanted to give ministers the power to cull animals only on the advice of vets and other experts.
But Ms Brankin assured MSPs that would automatically be done and did not need to be written into the Animal Health and Welfare (Scotland) Bill.
Amendments on the issue were put forward by the Greens, the Scottish Conservatives and the SNP.
Nationalist environment spokesman Richard Lochhead argued MSPs were being asked to rely on "an act of faith and the minister's word" that experts would be consulted before any cull.
His amendment demanded ministers first consider the impact on the economy and biodiversity before any slaughter is ordered.
He said measures must be in place to make sure the slaughter powers were not used in error.
Conservative rural affairs spokesman Ted Brocklebank put forward an amendment requiring ministers to take veterinary and scientific advice before any slaughter.
He said that, given the commitment on consultation there was no reason why the minister should not include it in the bill.
Green MSP Mark Ruskell lodged an amendment requiring ministers to take veterinary and scientific advice before culling animals who were disease-free and had not been exposed to any outbreak.
The powers would be used during an animal disease outbreak
"There are concerns here - it's worth putting in another check and balance," he told the committee.
Ms Brankin said: "Exercising the new powers would not be a response of first resort."
She said ministers had already made it clear that they would first have to establish the existence of a disease outbreak.
"In that, the role of veterinary and scientific advice is self-evident," she said.
"The powers are there for flexibility during potentially a complex exotic disease situation."
However, she said she would look at the possibility of creating a special document to set out the main factors that had been taken into account in deciding to exercise powers of slaughter.
Before Wednesday's meeting, Green MSPs and members of Advocates for Animals staged a demonstration outside the parliament in support of a complete ban on tail docking.
The bill as it stands would outlaw the practice, but an amendment has been submitted which would allow the tails of puppies to be shortened up to five days old, if a vet certified they were likely to be used as working dogs.
Mr Ruskell, who was among the campaigners said: "Removal of a dog's tail not only causes acute pain to puppies, but may also reduce the strength of the dog's back and compromise its balance and agility.
"Tail-docking is based on tradition whereas the latest scientific evidence shows that it is painful and causes long-term problems for the dog, be it a pet or a working dog."