The watchdog of the country's spying agencies has taken issue with aspects of their approach to getting warrants for intelligence gathering, under a new law passed last year.

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Inspector General of Intelligence and Security Cheryl Gwyn published a report today, in which she raised transparency issues in applications for spying warrants, clarity issues around authorisation of those warrants, and analysis issues in regards to the legal tests and thresholds under the Intelligence and Security Act.

The two spying agencies, the New Zealand Security and Intelligence Service (NZSIS) and the Government Communications Security Bureau (GCSB), were brought under that same Act in 2017 and single warrant regime was created for both to adhere to.

It's supposed to ensure New Zealanders' private communications won't be targeted, unless it is a matter of national security and a warrant is sought and then granted by both the responsible minister and a judicial commissioner.

All warrants are also subject to review and audit by the Inspector-General.

The report looked at warrants issued in a nine month period, from the entry into force of the Act on 17 September last year, to 30 June. During that time 40 warrants were issued, none of which were declined.

Most were for the collection of foreign intelligence, mostly outside of New Zealand, and intelligence on terrorism. A small number of warrants were issued for cyber-security.

Ms Gwyn said she did "not hold any warrant or warranted activity to be irregular," but she did raise issue with some of the these agencies' interpretations of what was required of them.

The law requires adequate detail be provided during a warrant application, explaining the agency's proposed activities and reasons for seeking it.

One of her concerns is the GCSB's applications for type 1 - the more serious - warrants.

Ms Gwyn said in some cases it uses "untargeted communications" which has the side effect of intercepting the communications of people about whom there are no national security concerns, alongside those it was looking for.

She said while the human rights of targets are taken into account, the rights of those affected by "incidental collection" are not.

"It makes no sense for the legal protection that comes from authorising interception to apply only when New Zealanders are targets, while New Zealanders of no security concern may have their commmunications intercepted without such protection," she wrote in her report.

The head of the GCSB Andrew Hampton said it's clear he and Ms Gwyn hold different interpretations of the law in terms of when a type 1 or type 2 warrant might be required.

"Like all Government Departments, where there is a lack of clarity around the law, we rely on Crown Law for a definitive view," Mr Hampton said.

"We have sought advice from Crown Law on this issue and will share it with the Inspector-General once it is ready."

Ms Gwyn notes too in her report, that differences in the interpretation of the new law is a sticking point.

In regards to the NZSIS, Ms Gwyn said she was "consistently concerned" the agency did not provide the level of detail she considered necessary. She raised particular concern about its applications for visual serveillance.

"NZSIS will sometimes have little or no information, when seeking a warrant, on what its best options and opportunities will be for carrying out an activity like visual serveillance," she wrote.

She also raised concerns with clarity around 'statements of purpose' for intelligence warrants, "these statements were almost identical from one warrant to another", and around who the warrant was targeting.

"For some classes of targets there was no detail at all on how the NZSIS proposed to collect information from them," Ms Gwyn said.

Director General of Security Rebecca Kitteridge welcomed the report, saying the NZSIS is committed to working with the Inspector-General and has responded to the questions and issues she has raised around warrant applications.

"I am pleased the report notes that since the period covered by the report, the Service has markedly shifted its approach to warrant applications and these changes go a long way toward meeting the concerns the Inspector-General has raised," Ms Kitteridge said.