The eight-page protocol also allows for the New Zealand Security Intelligence Service (SIS) to insist that hearings be relocated from a courtroom to any location or their choosing, or to require judges writing up their decision to only use a computer supplied by the intelligence.
Cate Brett, a spokesperson for the Courts, directed questions about the protocol to the relevant minister.
The processes and procedures adopted this week in Wellington were "required by law" and it was "not appropriate to a judge to comment on how a case is conducted", she said.
Andrew Little, the minister responsible for the courts and the SIS, issued a statement backing the handling of the case.
"There's a balance to be struck between the vital principal of open justice and the equally important need for national security to be maintained and I believe the current protocol achieves that balance," he said.
Thomas Beagle, the chairperson for the New Zealand Council for Civil Liberties, said the protocol showed excessive court processes were being dictated by the SIS.
"One wonders how all this pantomime hiding in shadows might subconsciously influence the judge - it would be hard to be properly sceptical in the face of this security theatre performance," he said.
"The procedures used for bringing this evidence into the court and presenting it to the judge show a lack of trust in the judge."
Wellington barrister Graeme Edgeler agreed, and said the courts should be properlyresourced to avoid having to outsource information-handling to intelligence agencies.
"The appearance of this is unsettling. The court is surrendering its control of court material to the Government, who are likely to be one of the parties to the case," he said.
Dunne used powers available to him under the Passport Act to cancel the woman's travel documents if he believed the passport holder was intending to take part in terrorism or the proliferation of weapons of mass destruction in a country other than New Zealand.
In earlier pre-trail rulings Justice Robert Dobson mulled the possibility of this classified information coming from agencies outside New Zealand.
The self-represented woman, whose identity is suppressed, is seeking a judicial review of Dunne's decisions, but has faced a legal labyrinth over the protocols which requires her to challenge the Minister's decision without being able to know why it was made.
In her absence the court has appointed special advocates - allowed to attend the secret closed hearings - to assist the court when considering the classified information.
The case is complex. The first scheduled date for a substantive hearing - in June 2017 - was abandoned and no new date has yet been set. An appeal lodged with the Court of Appeal by the women was then abandoned, and twice during the past year judgements have had to be amended and reissued.
MP Golriz Gharaman, the Green Party spokesperson for security and intelligence issues, said the court's acceptance of classified information in this one-sided fashion was unjust.
"The courts are asked to base their decision on so-called facts, presented by just one side. It's Kafkaesque – you can't answer the case against you, because you can't know the case against you," she said.
Justice Dobson, in his rulings on the case, and chief high court judge Geoffrey Venning, in a statement this week, have said while the closed-court proceedings are required by law they run counter to the well-established principle of open justice.
