The Ministry for Primary Industries is investigating after photos and video emerged of stock being hit while being loaded onto a live export ship.
Advocacy group Taranaki Animal Save took the footage of the animals, which were being collected by livestock carrier the Ocean Ute in Taranaki last week.
New Zealand exports live cattle to China in efforts to help the country build up its own herd. Last year nearly 135,000 cattle were exported there.
Group spokesperson Elin Arbez said what they saw last week was disturbing.
"Our activists captured footage of cows arriving at the gates of Port Taranaki with clearly visible circular bald patches on their bodies indicative of ringworm, and significant hair loss around the eyes as you see with lice/mite infestations.
"We also filmed cows being hit excessively with alkathene pipes and prodded with electric cattle prodders. Some of the cows were struck on and around their heads."
Arbez said to many breaches of New Zealand's Welfare Act are occurring on live export ships.
"We have obtained some of the voyage reports under the Official Information Act and they show that the animals suffer immensely on the journey.
"Isn't it enough that they suffer and die from heat stress, lameness, infections, necrotic wounds, broken bones, and more - must they also be beaten and afflicted with skin conditions prior to departure?"
Last year the government announced it would ban live cattle exports by sea - that ban is due to come into force in April next year.
But Taranaki Animal Save says the exports should be banned immediately.
The Ministry for Primary Industries (MPI) said it has received a complaint in regards to the loading of stock onto Ocean Ute and will investigate.
But MPI manager of animal health and exports Carolyn Guy rejected claims the animals were in ill health and that they will be subjected to immense suffering.
"MPI takes its responsibilities of animal welfare very seriously. MPI-approved veterinarians thoroughly inspect each and every animal before a decision is made whether or not it's fit to travel. Animals deemed unfit for travel are excluded from the export shipment.
"Animals with minor, treatable conditions - as will also be found on New Zealand farms - can be included in the shipment, and will be treated accordingly by the veterinarian on board the vessel."
She said for this shipment the export certificate application was for 5265 cattle but after the inspection, 4998 cattle were approved for the shipment.
"It is important to note that the circular bald patches can be indicative of ringworm, which is one of the most common skin diseases in cattle on New Zealand farms, particularly in younger stock. Ringworm is a superficial fungal infection, which is ubiquitous in the environment. The bald patches can remain for up to nine months after the infection has resolved following treatment."
To ensure animal welfare is key during the voyage, the on-board veterinarian submits daily reports to MPI - from the day the first animal is loaded until the last animal is unloaded at the destination port, Guy said.
"We also reject claims by Taranaki Animal Save that the voyage reports indicate immense suffering.
"The mortality rate for these shipments are extremely low. For all the voyages in 2021, the mortality rate was 0.07 percent - equating to 86 deaths out of 134,722 animals exported."