Inspector-General of Intelligence and Security Cheryl Gwyn is looking into whether New Zealand was involved in an American CIA detention and interrogation programme.
The details of the inquiry are outlined in the 2015 annual report of the Office of the Inspector-General of Intelligence and Security.
The United States Senate Committee Report documented instances of torture and inhumane treatment of detainees in the period between 2001 and 2009.
In her annual report, Ms Gwyn said there were a number of other countries involved with the programme - but the names were redacted.
"My decision... does not suggest or presuppose that New Zealand agencies or personnel were in any way connected with those activities.
"My inquiry, which is ongoing, includes an examination of whether there was any such engagement by the New Zealand intelligence and security agencies and whether there were and/or now are any safeguards in place or other steps taken to address any connection or risk of connection to such activities," she said in the report.
"To date, my inquiry has reviewed numerous intelligence community documents and is in the process of interviewing both past and present staff of the bureau (Government Communications Security Bureau) and service (Security Intelligence Service) who may have relevant knowledge and experience, and the agencies have assured me of their full cooperation."
It was important for the confidence not only of the New Zealand public but also for staff at the two organisations, who were required to work in complex and difficult environments, that there was appropriate guidance about the legal and ethical standards required of them, Ms Gwyn said.
The minister responsible for the GCSB and the SIS, Chris Finlayson, was asked if New Zealand had any involvement.
He said Ms Gwyn was undertaking the inquiry, and he would await the outcome of it before he commented.
The office's annual report also reports on potential breaches by the intelligence agencies, and the strength of their legal and procedural compliance.
It said the SIS still did not have proper compliance systems in place, a year after the Inspector-General first failed it.
In contrast, the GCSB, which was also found wanting last year, has been certified as having sound compliance procedures and systems in place.
In her annual report, Ms Gwyn said staff in both agencies had demonstrated a desire to comply with the relevant legislation, policy and practice.
She said the GCSB promptly identified errors and moved quickly to remedy them, and that errors during the past year "reflected inadvertence, unforeseen circumstances and/or simple factual or other mistakes".
"On that basis, I certify that the bureau [GCSB] has sound compliance procedures and systems in place."
Ms Gwyn said the SIS had "specific strengths in the warrant procedures and management of operational risk".
However the way it was structured meant staff could not ensure they were complying with legal and policy obligations.
"For those reasons, I cannot conclude that NZSIS had sound compliance procedures and systems in place.
"In expressing that conclusion, I want to emphasise the efforts made by NZSIS to institute changes."
Ms Gwyn office reviewed 15 interception warrants, 26 access authorisations and two director's authorisations from the GCSB during the year.
It also reviewed 29 domestic intelligence warrants from the SIS and two domestic visual surveillance warrants.
It said five potential breaches of policy, procedure or law were reported by the GCSB's compliance manager.
One involved a partner agency collecting metadata on a New Zealander and another where the GCSB picked up two communications from New Zealanders.
A third involved the targeting of a New Zealand permanent resident by a partner agency, without the GCSB's knowledge.
Ms Gwyn said in all cases the GCSB reported the incidents, ceased surveillance and destroyed the results.
She said they were all inadvertent, and required no further action.
Warrants not sent to office
Ms Gwyn also noted copies of the two visual surveillance warrants the SIS sought were not sent to her office, as should have happened. Instead, they were discovered during a regular review of warrants.
Her office had expected to monitor these warrants from start to finish, because they were the first of their kind to be issued under the updated Search and Surveillance Act, and because of their intrusive nature, she said.
"In response to that incident, NZSIS has now instituted appropriate arrangements to ensure that I am provided with a copy of any warrant issued on the day of issue or on the next working day, if it is impracticable to email on the day of issue.
"I expect to report on that review shortly and will address all of the requirements under the NZSIS Act for such warrants, including the extent to which those requirements - for example, meeting the standard of justification and minimising third party impact - are met in the inherently more intrusive and therefore more stringent context of visual surveillance."
Mr Finlayson said the report showed the system was working and that Ms Gwyn's position was not toothless - as some had asserted it would be.
"She's validly raised a very important issue on a reporting requirement that when something is to be done as soon as practicable, it doesn't mean forthwith, but it means getting on with it and they didn't and they're held to account."