A commercial fisherman is facing a fine of up to $100,000 and could lose his boat because of the deaths of 38 albatrosses.
The Ministry for Primary Industries (MPI) is taking action against the man who is accused of failing to use a mandatory device designed to scare birds away from baited hooks.
The commercial fisherman allegedly failed to use a line of streamers to deter the birds while fishing for southern bluefin tuna off the West Coast in April.
MPI said the prosecution sent a clear message that the rules need to be followed.
Its acting director of fisheries management, Steve Halley, told Morning Report 40 to 60 of the birds were accidentally killed every year, so they were taking this case very seriously.
Forest and Bird said the long line fishing industry needed to be better regulated to prevent the deaths of many more threatened and critically endangered birds.
The Ministry for the Environment's landmark environment report released last year said fishing by-catch is the main pressure on seabirds.
According to the report between 2001/02 and 2013/14 an estimated 55,000 seabirds were caught in fishing gear, although it said the estimated number of seabirds caught each year fell.
Mr Halley said non-compliance with the regulations was not acceptable.
"If there is sufficient evidence, prosecution action will be taken. MPI is now moving to put in place further mitigation techniques including mandatory use of line-weighting for all vessels using surface longlines."
MPI will also put placement notices on the higher risk vessels in the southern bluefin tuna fleet. The notices mean vessels cannot go fishing without an MPI observer on board.
However, Forest & Bird said it had been concerned for some time that the very low level of observer coverage in the domestic bluefin tuna longline fishing fleet had hidden the potential for extremely poor practice for avoiding seabird deaths.
The group's seabird advocate Karen Baird said the prosecution confirmed the need to have much higher levels of observer coverage of the domestic surface longline fishing fleet.
"MPI also needs to rapidly deploy electronic monitoring throughout the fishing industry to keep fishers honest," she said.
The Department of Conservation says it strongly supports the prosecution and works with industry to ensure proper processes are followed.
New Zealand waters are home to 14 different species of albatross, many of which are classified as being at risk of extinction.