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The letter comes after the High Court found last month that Minister for Agriculture Damien O'Connor, on the advice of the National Animal Welfare Advisory Committee (NAWAC), had acted unlawfully by not phasing out the use of farrowing crates and mating stalls.
SAFE chief executive Debra Ashton says the government needs to get serious about animal welfare.
"NAWAC failed to uphold the law, and mother pigs suffered as a result," Ashton said.
"We have animal welfare legislation for a reason, because we recognise that animals have needs. We are calling for better systems that will put animal welfare first."
NZALA president Saar Cohen said, "the judgement highlights the need to oversee NAWAC's actions and provide leadership and guidance to all animal welfare agencies."
"A parliamentary Commissioner for Animals will do that, as well as advocated for animals and ensure fair representation of animal interests in Government decision making."
NZALA and SAFE filed proceedings in February 2019 over O'Connor's and NAWAC's failure to phase out the use of farrowing crates.