A second complaint was made in April this year.
Waikato SPCA executive officer Sara Elliott-Warren said she could not answer any questions about a pending investigation and directed Hamilton News to the SPCA's national office.
RNZSPCA chief executive Ric Odom said complaints were received from a former staff member earlier this year.
"It covered a number of allegations some of which were around things the previous employee disagreed with and a number of items she alleges things we've done at the SPCA that shouldn't have been done," said Mr Odom.
"We have asked MPI for assistance if they can investigate those parts that, at least on the surface, relate to potential issues around practises.
"Like with any investigation you have to look at all of the facts. We've got one person's allegations. We've done a preliminary investigation on those. As a result of that investigation, we've said there are some things that refer to potential breaches of the Animal Welfare Act and then we asked MPI for their assistance. To be honest, we're a bit too close to it."
Mr Odom said MPI had not given him an indication of how long the investigation would take.
"These things take what they take. It entirely depends on what's uncovered, if anything at all. I understand their part of the investigation will commence very soon. It could even be as early as this week, but really it's entirely in their hands.
"The allegations have been made... we take any of those very seriously so that's why we decided to seek the assistance of MPI so that we can ensure that it's a completely unbiased investigation.
"Nothing is proven or otherwise at this stage. We're being ultra cautious in doing this and saying since the allegations have been made and since the initial investigation could neither prove nor disprove anything it was really important that we need to be seen to investigate this very thoroughly so that's what we're doing."
Mr Odom expects that MPI would report back at the end of the investigation and based on their report, RNZSPCA would assess their internal procedures if necessary.
MPI could not give an estimate about how long the investigation would take. Senior communications adviser Jim Flack said the time frame "depends on the complexity of the issue and the range of evidence. MPI is always thorough and doesn't rush investigations."