A commercial fishing company has been fined $12,500 and the skipper of its vessel ordered to do 40 hours community work, for fishing in a Marine Reserve.

Pursuit Fishing Limited and Nathan Marc Thomas, 46, were sentenced in the Westport District Court on Thursday following a successful prosecution by the Ministry for Primary Industries.

Both the company and Mr Thomas pleaded guilty to a charge each of commercially fishing in the Punakaiki Marine Reserve.

"Trawling in marine protected areas is prohibited. We expect commercial fishers to know where they are fishing and to follow these rules closely," says MPI fisheries compliance regional manager Howard Reid.

"Our digital monitoring of the commercial fleet, which tracks fishing vessels in near real time, detected this offending and should serve as a warning to all commercial fishers – we will take action when protected areas are threatened."

On April 14 this year, fishing vessel, the Marie Ann, skippered by Nathan Thomas went to sea from Westport to trawl for flat fish.

By April 17, they dropped their trawl net about 1.8km north of the marine reserve.

The crew headed south, entering the reserve, towing the net for the entire length of the reserve – about 11km.

Based on position reporting and information provided by Pursuit Fishing Limited, about 60 per cent of that four-hour trawl was through the Punakaiki Marine Reserve.

Their catch was 38kg of Gurnard, along with a small amount of rig and sole.

"Mr Thomas told MPI he knew he was fishing close to the marine reserve but thought he was outside the boundary and it seems this boundary was not marked on the vessel's electronic plotter.

"Our message is simple – mistakes come at a cost and we make no apologies for upholding the rules to ensure the protection of important marine reserves and other areas closed to fishing."

The Punakaiki Marine Reserve was established in 2014 and covers a total area of 3,520ha.

This reserve extends along approximately 11km of the coastline near Paparoa National Park, between Perpendicular Point and Maher Swamp, and extends about 3.7km offshore.

MPI encourages people to report suspected illegal activity through the ministry's 0800 4 POACHER number (0800 47 62 24).