The fishing industry says it supports observers on boats after revelations that some commercial vessels haven't let MPI staff on board.
The environmental lobby group Forest & Bird said it had obtained official data showing that 50 boats had refused observers over the past 18 months and that this illustrated the "industry is still plagued by rogue operators who appear to have something to hide".
Commercial vessels are required by law to allow observers on board but Forest & Bird say operators are using "manning limits" (effectively saying there is no room on board) to evade the rules.
Forest & Bird said that other operators were also using health and well-being concerns to not let observers on board.
"This calculated behaviour within the commercial fishing industry reveals an underbelly of lawlessness in a sector that has supposedly cleaned itself up," says Forest & Bird chief executive Kevin Hague.
"People will rightly be asking themselves, what's going on at sea that commercial fishers don't want the government or public to know about?"
"We know unlawful behaviour has been rife on some commercial fishing boats. The public deserves to know whether fishing crews are operating within the law, and this information certainly suggests that a significant number are not."
But chief executive of Fisheries Inshore New Zealand Jeremy Helson said the industry supported observers on its vessels.
Helson said that 9000 observer days were paid for by the industry in the past year.
Helson said the majority of cases highlighted in the Ministry for Primary Industries observer data related to "maritime manning limits".
"These are legal requirements around maritime safety which mean there is simply not enough room on board a small inshore vessel, that might have a crew of only one or two, for another body.
"However, in one case listed, the vessel owner had modified the boat to allow for another person aboard."
"Our skippers do co-operate in the vast majority of cases and relationships with the 100 or so observers are good.
"We don't condone refusal to carry an observer where there are no valid reasons."
The Ministry of Primary Industries has been approached for comment.