The environmental lobby group Forest and Bird has accused many fishing boat skippers of wriggling out of oversight by an observer from the Ministry for Primary Industries, despite having a legal obligation to do so.
The ministry has admitted this has sometimes been a problem, but only in a small minority of cases.
A cross section of fishing boats is required by law to have an observer on board to check up on environmental requirements such as not catching too many fish and not accidentally snaring species such as dolphins or albatrosses.
But skippers have in some cases avoided having any observer on board at all.
On some occasions, they point blank refused, in other cases they said there was no room on board their ship for another person.
One skipper objected to paying the cost of having to feed an observer, and in other cases, oversight was avoided by changing fishing methods from a targeted to an untargeted technique.
This information has emerged in material provided to Forest and Bird by the Ministry for Primary Industries under the Official Information Act.
It shows 50 cases of avoidance between August 2016 and February this year.
Some of those problems were patched up after debate between the ministry and the fishing company involved.
Others were not resolved and seven led to legal enforcement.
Forest and Bird chief executive Kevin Hague said this problem was serious.
"In a significant number of cases, 50 in the past 18 months or so, fishing boats have refused to have an observer on board," Mr Hague said.
"This raised the question what is it that they are trying to prevent being seen, what is it that they are trying to hide?
"We suspect that what they have to hide is an underbelly of illegal practise still occurring in our fishery."
Mr Hague said what enforcement the ministry had done was welcome, but more was needed.
"The observer is not discretionary, it is a vital part of New Zealand's attempts to have some kind of scrutiny of what is occurring at sea.
"We need to have maximum transparency, we need to step up to having cameras on all boats and to increase observer coverage."
The Ministry for Primary Industries said avoidance of ministry observers was not a problem for deep sea fisheries, but did happen with a minority of inshore fishing companies.
A senior manager, Steve Halley, said 100 observers do 9000 days of inspections across the fishing fleet per year.
But there definitely were problems in some cases.
"Occasionally, and it is a minority, we do have difficulty getting onboard some inshore boats.
"There are a range of reasons raised by the skippers, some of which, health and safety related, are probably legitimate, others not so much.
"And we take a pretty dim view of the not-so-much - that is where we use placement notices (enforcement) and if we have to, we take prosecutions and head to the courts."
Mr Halley said MPI had taken about 10 cases to court in a decade.
Over the last year it had put in 20 notices requiring a skipper to have an observer on board before they could sail.
"For the most part those are very successful," he said.
Mr Halley said around 30 percent of boats had an observer in low-risk areas.
In some high-risk areas, the percentage of boats with an observer on board was far higher, and had reached as high as 80 percent.
The cost of this is billed to the fishing industry.