Although major non-compliance issues had been found at the pound, the report concluded there was "no or insufficient evidence of breaches of the [Animal Welfare Act] in relation to the Napier City Council, the Animal Control Unit Team Leader or Animal Control Officer in the eleven incidents investigated".
This report's findings have been welcomed by the council, which is looking forward to putting the spectacle behind it.
Napier Mayor Bill Dalton said he was delighted that MPI "found that all dogs in our care were looked after appropriately".
"I'm also delighted that they found there was no evidence, or a lack of evidence of animal cruelty, so I'm delighted with the outcome."
Chief executive Wayne Jack - who faced personal criticism over the matter - said he was "absolutely" glad the matter was behind them.
"I think this has gone on for a long time, it's been very stressful for the staff who have been doing a fantastic job looking after animals and sometimes in quite difficult situations," he said. "But we can now move on."
This feeling was not shared by Animal advocate group Watchdog! - which laid the initial complaint sparking the investigation.
Yesterday spokeswoman Jessica Maxwell said she was disappointed that MPI had not found sufficient evidence.
"There was clearly a lot of stuff going on in that 11 incidents were investigated and while the executive summary concludes there is either no, or insufficient evidence, that doesn't mean to say they didn't happen, there was just insufficient evidence," she said.
Speaking of recent changes, and improvements at the pound, she was glad some good had come from the investigation.
"The pound had been run like the wild west, and I think it's brought Napier City Council
to realise that the public will not tolerate animal abuse."
"Watchdog! is very relieved that the main person under investigation is no longer employed at the pound."
The investigation was conducted between October and January, and involved interviews with all current and previous Animal Control staff, among other animal organisations.
It investigated 11 allegations which related to incidents between August 2015 and October 2016.
Only three of those allegations were made in the initial complaint - sent by Watchdog! asking for a formal investigation into the pound.
These included allegations that one staff member had failed to treat animals in his care appropriately, that occasionally he had treated dogs with inadequate consideration - such as leaving a dog chained up for some hours without food or water.
It was also claimed he seized two dogs which had mange and had not organised
any treatment for them in the 10 days they were in the pound.
The other eight allegations "came to light during the investigation".
In the MPI report, the senior investigator noted that a cross-over between alleged criminal activity and employment issues had been evident throughout the investigation.
So, the report had focused solely on the alleged breaches of the Animal Welfare Act.
"Hearsay in the form of rumour and supposition about these incidents has often been the predominant evidence of allegations amongst the large amount of material provided to this investigation," the report stated.
"Therefore the investigation has been limited to allegations which have direct evidence available in the form of either witnesses, CCTV or other evidence."
The 11 allegations investigated included the treatment of at least 10 animals, as well as the condition of kennels, and complaints of ill-treatment of animals by a person.
The person's name, like other parts of the report, was redacted under a section of the OIA.
The report summarised it had been a "complex investigation due to the need to separate fact from emotion, rumour and perception".
"This investigation has arisen because of an atmosphere of philosophical and personal differences that has beset the Animal Control Unit for some time.
"The unit was based and managed out of the main Council premise until relatively recently, this separation had blurred the lines of responsibility and control. The current management and adoption of specific roles has returned ACOs to their core business with clear procedures established."
It also noted nationwide concern there were no NZQA recognised qualifications for Animal Control Officers.
No Napier staff had formal training, apart from one person who had been trained as a SPCA Inspector.
"Variance in individual skill level can therefore place ACOs into the position where they may have to employ techniques they do not have the required skill level to execute. This places both the animal at risk of injury and the ACO at risk of committing offences under the Animal Welfare Act."
MPI Manager Compliance Investigations Gary Orr said the findings of the investigation put an end to many months of uncertainty.
"MPI is now able to close the door on this body of work and allow Napier City Council, and the public, to move forward with confidence."
Recommendations which were made to council in an earlier MPI External Audit Report had been actioned, or were in progress by the council - as reported in a revisit on March 16.
This report had found four major and two minor non-compliances, and was released to Hawke's Bay Today in January under the OIA.
These failures included a lack of standard operating procedures, a lack of evidence of training, a lack of documentation, poor ability to control temperature in the facility and a poor ability to prevent contagious disease.
While the overall management, supervision and operation of the facility might be compliant with MPI codes of welfare, the report said it was "a significant failure" that the situation could not be verified through documentation.