Shane Jones says his comments about a judge being a communist were taken out of context, but judicial decisions are "beginning to show elements of totalitarianism".
Attorney-General Judith Collins, the government's top lawyer, said she would speak to Jones about the comments.
The New Zealand Bar Association on Wednesday complained recent statements by ministers including Jones amounted to an attack on the judiciary, with president Maria Dew saying they could not be explained away as "political rhetoric".
At the same meeting with seafood industry representatives that recently saw Treaty Negotiations Minister Paul Goldsmith put under pressure, Jones had called High Court Judge Cheryl Gwyn a communist.
The comment was revealed in notes of the meeting, which was about the industry's concerns over the Marine and Coastal Areas Act the government plans to amend. Judge Gwyn had in March made judgments in favour of claimants, granting five Customary Marine Titles for areas on the Wairarapa coastline to Māori groups.
Heading into the debating chamber on Wednesday, Jones argued his comments were taken out of context and pushed back against the bar association's complaint.
"Oh look, I understand the bar association have an important role to play, but I wouldn't take out of the context one loose, humourous remark in a private meeting I didn't know was going to be leaked," he said.
"[They were] taking it out of context. I don't want to talk about the judge for fear of offending her sensibilities any more."
He complained about the notetaking by the Office for Māori Crown Relations - Te Arawhiti officials.
"I want those officials to be a bit more judicious in how they record the discussions. They made it sound as though there was some secretive, furtive agenda. It was a meeting in the diary."
However, he then spoke again about his views on the judiciary.
"This was a broad discussion that the creep of a lot of these judicial decisions is beginning to show elements of totalitarianism, and I don't like it," he said.
Collins was asked about Jones' comments, and said she had spoken to Jones before about the matter - and would again.
"As you know I take comity very seriously, I've written to my Cabinet colleagues earlier this year and I've since spoken to Mr Jones," she said.
The principle of comity sets out the boundaries of authority between Parliament, the government and the courts - with the Parliament making laws, the government administering them, and the judiciary interpreting and applying them.
When his latest comments about totalitarianism was put to her, she said: "I will speak to him. Thank you ... I think it's always better to keep the respect between the executive and the judiciary as it is between Parliament and the judiciary. I will be speaking to him further."
However, she rejected the suggestion Jones was out of control.
"No. Not at all."
Jones' leader, Winston Peters, backed his minister but mistook the question about his commentary on the High Court judge for Jones' commentary on the Waitangi Tribunal.
"Of course it's appropriate. They think they're the High Court of this country without ever being appointed to that job, they think they're a sort of House of Lords role, above being questioned. Excuse me, that's not what they were set up for in 1975 or later on by Geoffrey Palmer. It's got way out of hand ... now they're the judiciary are they? See what I mean? They were the tribunal."
Jones later said his comments were about democracy.
"What I mean is that we're going to change the law that pertains to the takutai moana [Marine and Coastal Areas] because that law has given a status to the Treaty that overwhelms our democratic right to not only redefine takutai moana but it restores back to the sovereignty of Parliament from the judiciary the meaning of the legislation. That's democracy."
He said his comment about totalitarianism was about the Waitangi Tribunal.
"The Waitangi Tribunal is elevating - and that's what I'm talking about - the status of the Treaty beyond Parliament, beyond democracy. I'm entitled to challenge that creep which I regard as happening in the Waitangi Tribunal is a type of antidemocratic totalitarianism."
Te Pāti Māori co-leader Debbie Ngarewa-Packer said the prime minister should be handling the matter - and if he would not, Parliament should do so through the privileges committee - which acts as Parliament's watchdog.
"I think if there's a disrespect from certainly that type of minister then there needs to be something done from within the Parliament and expectations of their conduct," she said.
"I think the prime minister should definitely take action but what it does put at risk at the House is that ... there is an expectation that the constitutional relationship and importance with the courts and Parliament is upheld. What we see here is a total disrespect to that relationship. So I think that is a privileges matter and it should be picked up by the prime minister.
"If we have a party - and indeed a minister - that's not going to respect the relationship with the courts then when and how is this place trying to take other parties to hold them to conduct and hold them to how they're meant to use their entitlement and privileges within Parliament?"