"Due to my limited time in the role and challenges to adequately resource the Office during the reporting year, I am not yet able to certify that either the NZSIS [the New Zealand Security Intelligence Service] or GCSB [Government Communications Security Bureau] has overall systems that are sound. That does not necessarily mean the compliance systems are unsound.
"While I am not able at this stage to certify the agencies' compliance, I am encouraged by the significant progress made by the GCSB following the Kitteridge report. The GCSB has devoted significant resources and organisational focus to compliance matters.
"During the reporting period, the NZSIS did not have an overall compliance framework or dedicated compliance and audit staff. However, the current Director has recently appointed a compliance advisor and made clear her intention to have a strong organisational focus on compliance matters, and I expect that progress will be made in the current reporting year."
Ms Gwyn, an experienced lawyer, took over the job of Inspector-General in May last year.
Her office has a larger, more proactive role as a result of GCSB reforms passed into law in 2013.
The reforms increased the scope and resourcing of the oversight regime, and came after a report by former Cabinet secretary Rebecca Kitteridge that found dozens of Kiwis could have been spied on illegally.
Revelations by Edward Snowden about intelligence gathering by the American-led Five Eyes spy system, of which New Zealand is a member, have kept the spotlight on the activities of intelligence agencies.
Today's annual report released today covers the period 1 July 2013 - 30 June 2014. Ms Gwyn said that she expects the report for 2014/2015 to be more comprehensive.
"My office is now well positioned to carry out a full programme of audit and review that is critical to effective oversight, in addition to strengthened inquiry and complaints work."
Green Party security and intelligence spokesperson Dr Kennedy Graham said the annual report exposed "big holes" in spy oversight, including that the NZSIS had no internal audit mechanism.
"The SIS can't be trusted to audit themselves. This strengthens the case for better parliamentary oversight of the spy agencies," Dr Graham said.
"The SIS and GCSB need rigorous oversight by a proper Parliament Select Committee, as the Green Party has repeatedly called for."
Dr Graham said the annual report was a "get out of jail free card" for the agencies, as the Inspector-General had been unable to carry out her necessary oversight.