The Ministry of Primary Industries says new animal welfare regulations will fill a gap between the Animal Welfare Act and Codes of Welfare.
As of Monday, 64 new animal welfare regulations were introduced.
Of the 64, 13 related to the transport of animals.
The new regulations were discussed at the Road Transport Forum Conference held in Dunedin last week.
Chairman of the National Livestock Transport and Safety Group, Don Wilson, of Pukekohe, said the ongoing consultation for the new regulations showed the transport industry's commitment to the correct treatment of stock.
''They [the regulations] will put a good emphasis on the farmer that they are going to present their stock fit to travel.''
Under the new rules, a farmer could be fined $500 for transporting an animal with a pre-existing condition without a vet certificate.
However, transporters can be fined $500 if an animal is loaded, unloaded or transported in a manner that causes injury, including back rub.
MPI manager of animal welfare sector support Leonie Ward said the ministry would continue training so that both transport companies and drivers were aware of the rules.
MPI had produced a range of information resources such as pamphlets and posters to be distributed in rural centres.
Changes to the Animal Welfare Act in May 2015 gave MPI the ability to make regulations under the Animal Welfare Act.
This meant MPI could better enforce the Act by setting out clear rules to protect animal welfare.
In April and May 2016, MPI sought feedback on the proposed animal welfare regulations.
Ms Ward said any severe offending would still be dealt with under the Animal Welfare Act.
''A lot of incidences don't justify a court case ... the regulations mean someone can receive a fine or infringement.''
For those already abiding by the Animal Welfare Act, the codes of welfare would produce few changes; however, a few regulations did set out new rules and requirements such as prohibiting tail docking on cattle and dogs.
Otago Federated Farmers dairy chairman Mathew Korteweg said the regulations would encourage assessing each animal individually rather than just as a group.
''Most farmers know themselves if a cow is fit for travel or not ... and if they can't there's still an option to get an animal checked if you were really not sure.''