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The AAL Brisbane had been targeted for full inspection by the Ministry for Primary Industries after a recent spate of live beetle finds on vessels arriving from Melbourne.
MPI chief executive Geoff Gwyn said the vessel was found to have an infestation of plague soldier beetles.
"It was found to be literally crawling with hundreds of beetles," Mr Gwyn said.
"The early warning shows our intelligence and surveillance system is working well and we are targeting vessels and cargo that have the highest risk."
The Ministry of Agriculture and Forestry said plague soldier beetles (chauliognathus lugubris) may be harmful to native New Zealand insects, and are also a potential carrier of diseases and other pests.
The insect's common name of plague soldier beetle is due to its habit of forming huge mating swarms.
The AAL Brisbane's operations were halted while the beetles were treated.
MPI is investigating to determine whether there have been any breaches of the Biosecurity Act 1993, and charges may be laid.