Judge James Rota closed the court to the public and media to hear the bail applications.
The decision to do so was made after "lengthy and strident" arguments in his chambers between himself, crown prosecutor Amanda Gordon and defence counsel Annette Sykes and Louis Te Kani.
Outside the court Annette Sykes, who told the Herald earlier that she was co-ordinating the legal defence for the people of Tuhoe iwi, slammed the way the police had handled the investigation, dubbed Operation Ate.
The notion that terrorism plots and military camps were taking place was a matter of police and media speculation.
None of the people she had dealt with had been charged with what the police were trying to investigate, she said.
"We have to ask ourselves why a piece of legislation [an anti-terrorism law drafted after the September 11 crisis] is hanging like the sword of Damocles over these people."
It was appropriate that the judge had conducted the hearing in a closed court, she said.
She praised him for "taking the heat out of this".
Six people appeared in the Auckland District Court yesterday on a variety of firearms charges, including possession of military style semi-automatic rifles, shotguns and molotov cocktails.
Five of them - four men, aged between 19 and 59, and one woman, 32, had their names suppressed by Judge Josephine Bouchier.
They were remanded in custody, without plea, until Friday, October 19.
A sixth person, Jamie Beattie Lockett, of Takanini, represented himself.
Lockett - also arrested in Auckland - said his arrest on firearms charges came at a bad time, as he was due to begin a private prosecution against "a senior police officer" today.
He told the court if he spent time in custody it would ruin months of preparation.
The summary of facts also contained errors, he said, and he claimed to have been "kidnapped" by police in three different locations.
He was remanded in custody overnight.
Police raiding a central Auckland house went armed with a search warrant for specific items, including body armour, military-style clothing and a silencer for a .22-calibre rifle.
One man was held in custody to Friday, but was granted interim name suppression while he told his mother of his arrest.
Four people - at least one a veteran activist - were arrested in Wellington.
One house that was the focus of an early-morning raid in the capital is described as a "second home" for anarchists.
The house - at 128 Abel Smith St in the central city - is an address frequently used for a range of activities, from yoga and film screenings to dance parties and meetings.
It is also popular as a hostel for travelling anarchists, and doubles as a bicycle repair shop.
Two of those arrested listed the address as their residence.
Others appeared in court in Hamilton and Palmerston North.
An Auckland resident got a shock when police raided his house in the early morning.
They busted down the door of his Grey Lynn flat about 6.15am.
They took a computer, books and photos from the room of his flatmate, who was not home at the time.
The man said he knew his flatmate was involved in "Maori and environmental issues" but the raid was still a surprise.
"I did think police were over-reacting.
"[The man] had a lot of activist friends around the country but I didn't know the degree [to which] he was involved."
A High Court hearing is to continue in Auckland today after an objection was raised to a police bid to seize computers.
Auckland Civil Liberties Union president Barry Wilson told the Herald that police would have to be "very careful before they started chucking terrorist labels around".
He said investigators should have decided whether charges should be laid under anti-terrorism legislation before launching the raids.
