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The Meat Industry Association says single-decked trucks are "not necessarily the silver bullet".
MPI data obtained under the Official Information Act shows more infringements for transporting a cattle beast, deer, sheep, goat or pig in a manner which causes back-rub were issued last year than ever before.
The 287 infringements in New Zealand last year included 46 in Otago and 36 in Southland.
Ministry animal welfare national manager Gray Harrison, of Wellington, said back-rub was an injury primarily seen in cattle.
Cattle sustained a back-rub injury when part of the animal — usually its highest point and on its rear end — rubbed against a stock crate when being taken to the meatworks.
"It can be nasty looking because it takes the skin off to bare flesh."
Regulations to fine transport operators for back-rub came in during 2018, he said.
Operators could be fined $500 if they transported an animal in a manner which caused injury.
A reason for back-rub was that farmers were breeding bigger cattle but the space available to transport them remained the same.
Double-decker stock trucks generally had a 1.57m-high lower deck and 1.4m-high upper deck.
Animals taller than 1.4m at the hip needed to be transported on the bottom deck or on a single-decked truck, he said.
Back-rub could be prevented by better communication between farmers, stock agents, meat firms and transporters.
Farmers with stock taller than 1.4m at the hip should tell their stock agent and transporter well in advance, so they could plan the best journey and select the right truck, he said.
Tall stock should be drafted into a separate mob before the truck arrived, so they could be loaded separately, he said.
If there were too many tall animals, then a single-decked truck might need to be dispatched to pick them up.
"You can prevent injuries and assist your transporter by picking up the phone. If they’re too tall, make a call."
Road Transport Association New Zealand senior industry adviser Jim Crouchley, of Ashburton, said the law stated a truck had to be no more than 4.3m high.
"Somewhere in between that you’ve got to squeeze in two decks of cattle."
On some double-decker trucks, the lower deck was taller than the upper deck, so there was no one-size-fits-all solution.
Truck drivers often arrived at farms with no prior warning of the height of the animals they were about to transport.
A way to stop back-rub was to use single-decked trucks.
"The very simple solution is to single deck the cattle but you’ll be struggling to find a meatworks that wants to do that."
As meatworks were paying the transport costs, he doubted they would want to pay twice as much.
Meat Industry Association chief executive Sirma Karapeeva said a single-decked truck was best for tall animals, otherwise they should be loaded on the bottom deck to minimise the risk of back rub.
"However, transitioning to single decking is not necessarily the silver bullet."
Mandatory single-deck transportation for all cattle would have a significant economic impact on farmers as well as require additional trucks on the road, she said.
The sector was committed to constructive relationships with transport firms and its members encouraged transporters to proactively raise such issues with them prior to the livestock being picked up, she said.
Animal welfare was paramount for the sector.
"With a greater dairy beef influence, the size of the cattle has increased over the years and this is a factor in causing back rub during the transport of animals," she said.
"We believe the back rub issue can be resolved with better communication between farmer, the buyer or processor and the transporter. Ultimately, it is the responsibility of transporters to ensure tall stock have enough room ...
"Farmers that need to transport tall stock should speak to their transporter or stock agent so they can plan the journey appropriately and send a suitably configured truck."