A group representing the commercial fishing industry says it's "not excusable" some skippers are fishing in protected areas.
It comes as data obtained under the Official Information Act shows the Ministry for Primary Industries (MPI) is investigating a set netting vessel in the South Island.
It alleges it fished in both a dolphin-protected area and a marine reserve.
Seafood NZ says it's working on a solution to ensure companies know the rules about not fishing in these protected areas.
"It's not excusable at all," chief executive Dr Jeremy Helson says. "We will work with MPI and the companies to make sure skippers and crew understand their responsibilities."
In December last year, new electronic monitoring rules came into place for 860 commercial fishing vessels, meaning the movements of vessels were tracked by the Ministry for Primary Industries.
Skippers were also expected to report their catch every day electronically, a vast change from a paper-based reporting system that's been in place for decades.
Since the requirements came into place, there's been 10-times the amount of offences picked up by MPI when compared to 2018 when the technology was not widespread.
"It's definitely increased," MPI national manager of fisheries compliance Steve Ham says.
"It comes down again to we're seeing more, and when we see more we have to deal with more. It's created a lot of efficiencies for us within fisheries. Compliance is a big part of fisheries management."
Around half of the offences are lower level, like not reporting catch correctly or on time due to faulty equipment.
However, MPI says at the more serious end, non-reporting can also be "deliberate".
Some of the more serious breaches include vessels fishing in marine reserves, Benthic Protected Areas or inside exclusion zones, set up to protect marine mammals.
Dr Helson says most skippers have embraced the change - but mistakes can occur.
"It may be that they haven't updated their onboard systems, maybe their charts are a little out of date, or maybe they're just being careless. Whatever the reason, I think it needs to be addressed."
Sealord, one of the country's biggest fishing firms, has been implicated in serious offending after the Ocean Dawn trawler strayed into a protected area off Christchurch in 2018.
This year the company was fined $24,000.
Sealord CEO, Doug Paulin, says it's disappointing it happened but says it was a genuine mistake. He says the company has invested in new technology to ensure it doesn't happen again.
Paulin says this includes installing "geospatial alarms" on vessels, so skippers are alerted when they get close to a protected area.
For 2020, even though COVID-19 left some vessels tied up, MPI expects to launch 20 prosecutions.
"As education gets better, as technology gets better, then you'll see these numbers continue to go down over time," he says.
Ultimately, Paulin believes, no one goes to sea intending to fish in protected areas.