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The protest was the first action in an ongoing campaign to persuade the university to change the focus of the new research facility, New Zealand Anti-Vivisection Society (NZAVS) campaign manager Tara Jackson said.
NZAVS wanted the university to end its use of live animals and to use the building for non-animal-based research.
"It’s prolonging inaccurate, unreliable, unnecessary research," Miss Jackson said.
The university responded yesterday it only used animals where there were no alternatives, and they were not subjected to pain or distress.
Miss Jackson said the university still used live animals to train medical students, when Canada and the United States had moved away from the practice.
That showed "how far behind they are in terms of research".
"We don’t even have to argue the ethical side, it’s so obvious. We are trying to argue for good science."
As the protest marked the group’s first organised action against the use of animal-based research at the facility, she was pleased with the turnout.
"As a first action this is awesome," she said.
"The opposition is growing.
"There are loads of people from all around New Zealand that are keen to get involved."
Two Campus Watch staff watched over the protest.
A police spokeswoman said there were no issues reported with the protest and no police attendance was required.
Miss Jackson said more action would follow, but NZAVS was yet to confirm what that would be.
University of Otago deputy vice-chancellor for research and enterprise Prof Richard Blaikie said the university was investing in the new facility to maintain animal facilities of the highest international standard.
"As permitted through the Animal Welfare Act, the use of animals in research or teaching to enhance human or animal health, or the management of the environment, requires us to ensure the needs of those animals are met in accordance with both good practice and scientific knowledge," he said.
The university kept up to date with leading developments, and required the use of non-animal alternatives when those were available, including computer or physical models, tissue or cell cultures, human-participant research and simulations.
"There are simply no feasible alternatives ... for many complex biological studies or the development of new therapies.
"Our research is helping to contribute to new alternatives in many cases, and as these are validated and become available they are adopted, as required by our commitment to reduction, replacement and refinement of animal use wherever possible."
In the limited cases where live animal use in teaching was justified and approved by an animal ethics committee at Otago or another New Zealand university, animal welfare was of the highest priority, Prof Blaikie said.
"Animals are not subject to pain or distress through the use of proper handling methods or modern anaesthetics, similar to a hospital setting."
The facility is expected to be completed in February 2018.