The charges carry a maximum penalty of five years in prison, and a potential fine up to $250,000.
Judge Jan Kelly said the offending arose amidst an illegal fishing operation in the Chatham Islands, and happened between 2017 and 2018.
Clarke, who was a commercial fisherman in the islands, provided fish to a seafood company. After the fish was received, the company's director and Clarke would allegedly come to an agreement on how much of the haul, if any, was to be reported, Judge Kelly said.
The director is due to go to trial over the case.
In all, 11,038kg of rock lobster and pāua went unreported. The total benefit to Clarke is estimated to be $340,000, but the total value of the unreported fish is believed to be about $885,000.
The "significant illegal fishing operation" began after fisheries officers checked some of Clarke's holding pots and found a "significant quantity" of pāua for which no catch or landing returns had been completed.
Judge Kelly called the offending "unprecedented".
"The ministry has been unable to find any cases where the total quantity taken comes close to the amount of the present case."
Reading from victim impact statements, Judge Kelly said the local iwi trust was now working to rehabilitate the "important fishery".
"The iwi trust says it has zero tolerance and strongly condemns Mr Clarke's illegal activity, and expresses deep disappointment that a resident would commit such offences."
His actions undermined the objectives of the quota management system and undercut legitimate product.
Defence lawyer Alwyn O'Connor said Clarke "appears embarrassed and ashamed before the court" this morning, offering his "sincerest apology to the community for his wrongdoing".
He was supported in court by his fiance of 19 years.
Clarke has agreed to give evidence in the future trial for his alleged co-offender.
A pre-sentence report revealed Clarke had been suffering from anxiety, "fitful and erratic sleep patterns" and "ruminating thoughts" in the lead up to his sentencing.
He told probation the offending stemmed from financial problems caused by his bankruptcy in 2013 and the legal fees to have his bankruptcy annulled in 2016.
"He estimated much of the money he received from illegal fishery and fishing was to have his bankruptcy annulled."
Judge Kelly allowed discounts to the sentence for Clarke's guilty pleas, remorse, and assistance to the prosecution, as well as a small discount for his mental health.
She sentenced him to nine months of home detention, which he will serve away from the Chatham Islands.
He must also do 200 hours of community work.
Orr said it was important to note the starting point of the sentence - before discounts were applied - was four years in prison.
"I thought that was a fairly powerful message from the court and provides a lot of support for what we do," he said.
Vessels and other equipment will be seized to pay for the "deemed value" of the unreported fish.
"I've been in fisheries enforcement for over 20 years and I've never experienced anything of that scale before," he said.
"This has been undertaken by somebody who's been a member of the Chatham Islands community for many years. You've heard the condemnation from iwi and from the commercial fishing representatives. It's just inexcusable and it really goes to the foundation of trying to manage two stocks . . . that are under stress."
When MPI officers originally found Clarke's unreported catch, there was half a tonne in his holding pots.
"It was like sort of picking on a loose thread. We started pulling on that. The more we pulled the more we uncovered. Subsequently that half a tonne turned into 11 tonne of unreported fish, which is huge by anyone's standards.
"You can make a good living out of legimately catching rock lobster and pāua around the Chatham Islands. There's no need for this."
