The worst result, an 87 per cent compliance rate, was with passengers who were checked after having passed through a full customs inspection.
MPI said Christchurch's performance was at least partly driven by a lack of national consistency in application of requirements.
It ordered an immediate investigation into the reasons for the poor outcome.
Another recommendation was the need to further consider the level of risk that some slipped goods represent to New Zealand.
MPI also recommended that a competency review and/or refresher training be carried out at Christchurch on requirements and how to conduct a full search.
The overall shortfall in compliance across all airports was mostly due to low-risk items like airline food packets and dirty shoes getting past biosecurity checks, says Roger Smith, deputy director general of verification and systems.
"In a number of cases, these items were only slightly contaminated, or were unlikely to have been exposed to biosecurity risk - such as toiletries containing honey."
He said MPI had started implementing recommendations from the survey to improve compliance, including looking at additional staff training where needed.
Auckland, Christchurch and Wellington airports accounted for 97 per cent of air passenger arrivals.
Over the survey period 243,764 passengers and crew arrived at the three largest airports.
Of these, 80 per cent were cleared in Auckland, 13 per cent in Christchurch, and 7 per cent in Wellington.
At Auckland, 4330 passengers were surveyed, 2836 at Christchurch, and 965 at Wellington.
Christchurch Airport have not yet commented on the survey.
