The incursion into the off-limits zone was detected by digital monitoring which tracks vessels in real time.
On April 14 this year the fishing vessel, the Marie Ann, skippered by Thomas went to sea from Westport to trawl for flatfish.
Three days later the crew dropped their trawl net about 1.8km north of the marine reserve, then headed south and entered the reserve.
The vessel towed the net for the entire length of the reserve – about 11km.
Thomas told MPI he knew he was fishing close to the marine reserve but thought he was outside the boundary.
MPI said it appeared the boundary was not marked on the vessel's electronic plotter.
Based on position reporting and information provided by Pursuit Fishing Ltd, about 60 per cent of the four-hour trawl was through the marine reserve.
During the trawl, they caught 38kg of Gurnard, plus a small amount of rig and sole.
MPI said its role was to uphold the rules to make sure marine reserves and other areas closed to fishing were protected.
The Punakaiki Marine Reserve was established in 2014 and covered an area of 3520ha.
The reserve extended along 11km of the coastline near Paparoa National Park, between Perpendicular Point and Maher Swamp, and about 3.7km offshore.
