High security closed court hearings are rare but a process for one type was laid out in a case about a passport being cancelled on security grounds.

A secret hearing was being held under tight security at the High Court in Wellington on Wednesday.

The case was so secret that it was not listed in any form on the court's list of fixtures for the day.

Access to the basement level courtroom was barred by court and other black-clad security staff. The usual access between a public cafe on that level, and the court building, was also stopped.

The court manager, Jane Penney, said Justice Robert Dobson had directed that it was a closed court, and media could not attend.

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It is rare for hearings to take place without being publicly listed, even if only in a form that does not name individuals.

Last April though, the same judge who was hearing Wednesday's case laid down a security procedure that was to be followed in a case in which a woman was challenging the cancelling of her passport.

She was living in Melbourne, Australia, at the time.

Classified security information was given as the reason for cancelling her passport. The law allowed for the information to be given to the court that was to hear the woman's challenge, without the woman herself being told what the information was.

"This information is to be conveyed in the absence of the appellant, any counsel representing the appellant and members of the public," the judge had summarised.

The protocol to be followed in such cases was agreed with the Chief Justice, Dame Sian Elias, and the Attorney-General, Chris Finlayson, in January 2017, to allow for the one-sided provision of classified security information to a judge deciding a case, and to protect the information from any inadvertent disclosures.

The law used to cancel the woman's passport was an interim measure now replaced by parts of the Intelligence and Security Act 2017.

The law used in the woman's case concerned people who it was alleged were a danger to the security of New Zealand or another country and cancelling their passport would prevent them carrying out or facilitating an action.