"Once that is done, we will be looking for any evidence of offences under the Animal Welfare Act."
Mr Mikkelsen said their top priority was to figure out whether there had been any suffering.
Their investigation would also take into account the cause of the fire, which is yet to be determined by authorities.
This morning's blaze is at least the third large fire of its kind at the farm.
Last August, about 400 mother and baby pigs were burned to death in a blaze on the premises, a few weeks after new owners started at the farm.
In 2005 -- under different owners -- up to 300 animals were killed in a similar fire.
Animal rights group SAFE said it was "horrified" that dozens of pigs had been burned to death at the farm, just north of Ngaruawahia.
SAFE executive director Hans Kriek said the group was calling for mandatory sprinklers to be installed in all factory farms.
"It is clear that fire prevention measures are woefully inadequate on this farm and it appears that nothing has been learned from these previous disasters.
"On factory farms, there is not escape for the animals. They already suffered from cruel confinement and now they have had a horrifying death," Mr Kriek said.
The SPCA said the fire highlights the need for animal emergency planning.
"This tragedy is a timely reminder that farmers and others working with animals must have robust animal emergency management plans in place. At the very least, farmers should have effective smoke alarms, fire extinguishers," said Ric Odon, CEO of SPCA NZ.
Earlier today, a witness told the Herald the fire had been ongoing since just before 8am.
The witness said he felt bad for the animals and also for the farmer, who was fairly new in the area.
"It's just a sad thing for the pigs. We feel sorry for the pigs and we feel sorry of the farmer."
Although the cause has not yet been revealed, the man said he suspected rodents may have contributed to it.
"You've got an environment with pigs and so there's rats -- rodents are the worst thing that we (farmers) worry about. They chew in the wiring and can cause electrical problems. That's just one possibility."