Before the vessel left port, Environment Southland received information that undaria was growing on its hull.
An inspection by divers at its mooring in Deep Cove on November 20 confirmed the presence of the invasive weed.
Two days later, the regional council issued Clark with a notice directing him to return the vessel to Bluff by December 7, but he did not do so until December 16.
The Biosecurity Act requires vessels entering the Fiordland marine area to meet cleanliness standards, and the regional council's pest management plan requires vessels to be free of undaria when entering the marine area.
Clark admitted a charge of failing to comply with the notice of direction, which carries a maximum penalty of three months' prison or a fine of $50,000, as well as two charges of failing to comply with the regional pest management plan.
Defence counsel Ben Alexander said the defendant cleaned the vessel's hull before departing for Fiordland and believed the undaria had grown in the period between then and the inspection.
He had returned home to Athol after the trip, and could not return to Fiordland to relocate the boat during the first of two weather windows.
He did make an attempt during the second weather window, but rough conditions and his relative inexperience as a skipper had forced him to turn back.
Clark was "not blasé" about his responsibilities, and his actions were neither intentional nor reckless, Alexander said.
Environment Southland counsel Tim McGuigan said Clark had shown a "high degree of carelessness".
His claim to have cleaned the boat before departing Bluff was inconsistent with the amount of undaria on the hull when it was inspected, McGuigan said.
Judge Brandts-Giesen said the defendant "either did not look properly for contamination on his vessel or proceeded regardless".
He then failed to relocate the vessel himself, or employ an experienced skipper to do so, during the 14-day notice period.
In settling on the fine level, he took account of the defendant's early guilty plea, expression of remorse and previous good character.
He hoped the case would serve as a warning to all vessel owners.
