The Ministry of Health wanted to implement daily saliva testing in quarantine facilities in January this year - but six months later it remains infrequently used.
It is now facing criticism - which it rejects - that it has been the main obstacle to rolling out the testing in MIQ facilities because of the technical advice it has given to Covid-19 Response Minister Chris Hipkins.
A saliva PCR test is far less invasive than the nasopharyngeal PCR test, but there are conflicting views on whether it is sensitive enough to become the main form of testing.
Saliva tests have been pushed for since last September, when a review by Sir Brian Roche and Heather Simpson said it should be introduced as soon as possible.
So far, more than nine months later, only 394 tests have been conducted - almost all of them in the Jet Park quarantine facility.
This week Hipkins stressed his own frustrations about the lack of a rollout of saliva testing for border workers, while an independent advisory group - chaired by Roche - has called for it to be the main form of testing.
Ministry of Health documents - released to National MP Chris Bishop under the Official Information Act - show that the ministry wanted daily saliva tests in January for workers in MIQ facilities with quarantine wings.
This was ready to be rolled out on a voluntary basis to supplement - but not replace - the standard nasopharyngeal PCR swab.
It aimed for 80 per cent update by the end of the first month - or 2160 workers out of an estimated 2700 quarantine wing workers. But by February 17, only 170 samples had been collected.
Bishop said it was almost comical to consider how long it had taken to come only so far.
"Ten months after the Roche/Simpson report, we still don't have a timeline for saliva testing to be rolled out nationally, even though leaked emails show border workers desperately want it."
Meanwhile Rako Science, which provides saliva testing to Air NZ, is accusing the ministry of using its own "'expert advisers' who went out of their way to cast doubt on Rako's science".
"We were not given the chance to challenge their multiple major errors, or to support them to get their own work and advice right," Rako Science director Leon Grice said.
"The ministry has consistently advised Chris Hipkins incorrectly - that saliva is a less sensitive sample for detecting Sars-CoV-2 as compared to nasopharyngeal swab tests."
He said the company's protocols had been "diagnostically validated" as "at least as sensitive and accurate as nasopharyngeal swab tests".
"Rako Science has tremendous sympathy for Minister Hipkins having to base his decisions on inadequate advice from expert advisers, fixated on trying to develop and deploy their own saliva test."
This comment was directed at the ministry's decision in May to contract Asia Pacific Healthcare Group (APHG) for saliva testing at MIQ sites, even though Rako's is the only diagnostically validated saliva test in New Zealand.
The ministry has said it went through a comprehensive procurement process before contracting APHG.
A spokesperson for the ministry said it continued to be in discussions with Rako Science.
"The science and application of saliva testing continues to evolve. Our advice to Minister Hipkins continues to reflect this evolving science."
A spokesman for Hipkins declined to comment on whether he had been poorly advised, saying only that the minister wanted more saliva testing - but it was too early to say if it should be the main form of testing for border workers.
Hipkins has previously suggested worker reluctance playing a role in the low use of saliva testing, as workers need to be free of smoking, eating or drinking for half an hour before being tested.
He has also said there is no barrier from his end to wider use of saliva tests at the border.
A public health order in April paved the way for saliva testing to be used for a border workers' mandatory regular test.
But it needs sign off from director-general of health Ashley Bloomfield, who is yet to provide it.
A ministry briefing to Hipkins on April 30 did not recommend saliva testing for symptomatic cases or as the main surveillance testing tool.
It also disagreed with advice from the independent advisory group, chaired by Roche, that saliva testing should be rolled out as the main method of testing.
"A substantial proportion of Covid-19 participants in Jet Park test negative in their saliva for Sars-CoV-2 (25 to 42 per cent, depending on the saliva PCR method) which is a warning sign that saliva testing may miss certain Covid-19 cases under certain circumstances," the ministry said.
It did, however, recommend that workers needing a weekly test could have a nasopharyngeal PCR test once a fortnight, and a saliva test every two to three days.
"Saliva PCR testing is considered slightly less sensitive than nasopharyngeal swabs. However, advice from the New Zealand Microbiology Network and our epidemiologists, based on international and New Zealand-based validation data and research, is that increasing the frequency of testing will increase the overall sensitivity of the testing regime," the ministry said.