Another dive charter operator heading from Tutukaka to the Poor Knights also suspected Extreme Lights was inside the restricted area.
McQuarrie continued hauling in fish, despite warnings about being in the marine reserve and berthed at Tutukaka later that day, where the catch was unloaded and sold.
An investigation by Fishery officers found Extreme Limits was between 700 and 800 metres inside the commercial longline restricted area which is one nautical mile around the islands.
McQuarrie told MPI the GPS data from the dive charter operators did not appear to have been calibrated and may have been unreliable. MPI then obtained a report from a geodetic surveyor who concluded the GPS systems were correct.
McQuarrie pleaded guilty and said although he did not intend to fish inside the prohibited area, he had failed to take all reasonable precautions to prevent an offence from occurring.
In court on Friday, MPI prosecutor Angus Wood said McQuarrie was well aware of the prohibited area as he had fished in the area previously and had electronic devices on board.
Judge Keith de Ridder said it was not a case of Extreme Limits inadvertently drifting in a prohibited area.
McQuarrie was fined $7500 and ordered to pay $3200, which was proceeds from the sale of fish, plus a further $15,000 in redemption fees.
The redemption fees are paid to MPI for the possible return of Extreme Limits to its owners, who were not at fault in McQuarrie's offending.
The vessel is worth $330,000.
Conservationist Wade Doak said: "One episode like that shows what [would happen] if it was not severely policed."