Those animals suffering most harm dropped from the long-term average of 6.6 per cent to 5.1 per cent.
Stock survival rates were 96.2 per cent because the experiments were minimally invasive and they generally stayed with their herd.
However, just 3.3 per cent of rodents and rabbits survived their experiments.
MPI noted the rolling three-year average, at 253,215, was at its lowest since the Animal Welfare Act 1999 came into force.
"There are strict controls around the use of animals for research, testing and teaching," said MPI's Paul Dansted.
"These controls are designed to prevent unnecessary pain and distress to animals and ensure any cost to the animals must be outweighed by the potential or actual benefits to be gained from the work."
- AAP