The Ministry for Primary Industries has acknowledged it needs better processes on identifying commercial fish dumping.
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A fisheries inspector's report leaked in May said the ministry's inaction was making dumping and overfishing worse.
At the time, the ministry said it was prosecuting 300 fisheries cases a year. But figures released under the Official Information Act showed there had been just 28 dumping prosecutions since 2004.
Ministry national compliance operations manager Gary Orr told Morning Report about a third of the annual 300 cases related to unauthorised discharging of catch by commercial fishermen.
The term dumping was a specific charge under the Fisheries Act and required a very high threshold of evidence.
"It basically means you have to have almost eye-witness testimony."
But there were alternative charges which did not require such a high threshold, such as submitting false or misleading information in catch returns.
"For us to prosecute a commercial fisher for dumping requires a very high evidential threshold"- Gary Orr
Mr Orr said it was difficult to determine exactly how many prosecutions were for commercial fish dumping.
"Our databases aren't set up to be that definitive.
"What it does is record the offence but it doesn't record the circumstances of the offence.
"What it would require us to do is to open up each individual case and look at those circumstances."
Mr Orr said commercial vessels would soon have electronic catch reporting, and GPS tracking devices and cameras would eventually be on board boats.
The ministry set up an independent inquiry in May into claims it did not prosecute skippers for dumping fish despite having video footage. The inquiry is headed by former Solicitor-General Michael Heron QC.
Data provided by the ministry under the Official Information Act showed that from 2004 to 2015 there were there were 105 charges at the lesser threshold of submitting false or misleading information, but indicate there were few separate prosecutions.
The 105 charges related to five offenders convicted of multiple charges, one of whom was a recreational fisherman, and 85 appeared to be against just one offender.
The OIA figures showed that in 2011 there were 107 successful charges against commercial operators; 13 of those were against two operators for submitting false or misleading information and there were none for dumping.