An animal welfare inspector has been fired after secretly recording his colleagues during an investigation into the case of three crocodiles found at a Humpty Doo high school.

Key points: In 2016, three saltwater crocodiles were dumped in a school administration office

In 2016, three saltwater crocodiles were dumped in a school administration office Animal welfare inspectors disagreed about the course of the investigation

Animal welfare inspectors disagreed about the course of the investigation Inspector Lucas McAuley secretly recorded conversations with colleagues, and sent these to his superiors

Lucas McAuley had his application for unfair dismissal remedy against the Northern Territory Government Department of Primary Industry and Resources rejected by the Fair Work Commission on January 24.

But he is appealing the decision, and a hearing date has been set for April 4.

In the January decision, which was published this month, Commissioner Nicholas Wilson noted the irony that secret recordings Mr McAuley produced to argue his case then became a key part of the evidence against him.

"The irony is not lost upon the commission that one of the key reasons for Mr McAuley's dismissal, namely that he covertly recorded conversations with co-workers without their knowledge or consent, is part of the evidence brought against Mr McAuley in relation to his conduct," he said.

The decision also noted that Mr McAuley, who is a former police officer, said he made the recordings to "protect his interests" in the event of a lawsuit, or if he was fired for unjust reasons.

The animal welfare inspector's unravelling began on Sunday August 21, 2016, when three emaciated female crocodiles were found in an office at Taminmin College, Humpty Doo, 30 kilometres from Darwin.

The crocodiles were put there by four youths, but it was believed the crocodiles had first escaped from a crocodile farm.

CCTV footage of the four people who set three saltwater crocodiles loose in a school administration office in 2016. ( Supplied )

Tasked with investigating the incident, Mr McAuley sought to get a search warrant under the NT Animal Welfare Act to enter Darwin Crocodile Farm.

The decision noted this was becasue the farm was less than a kilometre away from where the boys told police they captured the reptiles, so Mr McAuley reasoned it was a likely source of the crocodiles.

However others believed markings, similar to brands, on the animals showed they were from Crocodylus Park.

Despite seeking legal advice from lawyers who at the time believed getting a warrant would be a good idea, Mr McAuley's superiors then decided that a "friendly visit with the view to educating" the Darwin Crocodile Farm would be a better move.

One said she believed it was a leap "between the crocodiles having escaped and the view that the circumstance amounted to an animal welfare problem".

Mr McAuley did not agree.

Recordings emerge

He made contact with the Commission for Public Interest Disclosures with allegations that officers within his department had "breached their obligations with respect to the crocodile investigation".

A few days later he contacted his department's CEO Alister Trier and deputy chief executive Ian Curnow, saying he had "serious concerns about unethical behaviour that goes against the departments values" among some of his colleagues and superiors.

That is when he also sent a USB containing secretly taped recordings with his colleagues.

Yet when the chief executive replied, he said he found no evidence to support Mr McAuley's allegations, but would instead launch an investigation into Mr McAuley's conduct, given he had made secret recordings.

An independent investigator was then appointed, and after its final report was delivered, Mr McAuley was fired for misconduct on July 26 last year.

The Fair Work Commission noted it found the secret recording of co-workers to be "sneaky, abhorrent, a fundamental breach of the relationship of trust and confidence between employer and employee, and a valid reason for the termination of employment".

But Mr McAuley defended his actions, stating they were made for his own notes to "protect his interests" — as a civil case had been brought against other officers in the department for an unrelated matter, and as he believed superiors were planning to stand him down for mental health reasons.

He also said his superior's encouraged the use of voice recorders, but the commissioner rejected "the proposition that somehow departmental officials had permitted the making of secret recordings by Mr McAuley or others".

Mr McAuley could not be located for comment.

The Department of Primary Industry and Resources was invited to comment, but did not respond.