"We informed industry prior to the start of the season of our hard line on cargo vessels believed to be infested with stink bug."
The vessel, which was carrying vehicles from Europe and the United States, left Auckland earlier this afternoon.
On September 1, a new import health standard came into force, meaning tighter rules for importing vehicles and machinery – particularly around treatment and cleaning.
Gilbert said the vessel will now need to be treated off shore before it can return.
"If permitted to come back, the vessel should also expect intensive inspection before we allow any cargo to be discharged," Gilbert said.
In April the MPI came out and said more than 2000 stink bugs had been found on four car carriers coming from Japan since February, resulting in 8300 vehicles being turned away.
The pest has the potential to destroy New Zealand's fruit and vegetable industry and is resistant to many insecticides, making it difficult and expensive to control.
Kiwifruit, apples, apricots, pears, vegetables, wine, other fruit and plant seeds are most at risk in New Zealand.
Paul Hallett, MPI manager facilities and pathways, said imported vehicles and machinery pose a high biosecurity risk.
"Imported vehicles and machinery pose a high biosecurity risk, as stink bugs hibernate in nooks and crannies during the northern hemisphere winter.
"We want to do everything we can to stop brown marmorated stink bug from invading New Zealand, given the damage it could cause to our horticulture industry."
This period of time is known as the "risk season" when stink bugs from the Northern Hemisphere are most likely to crawl into cargo heading to New Zealand.
Kiwifruit Vine Health chief executive Stu Hutchings said the impact from the bugs could be massive for the local industry.
"This could wipe income of growers and have an impact on GDP of between $1.8 billion by 2038," he said.
"The horticulture sectors' export value could fall by up to $4.2 billion."
