New COVID-19 testing rules for people working at New Zealand's border are coming into effect on Sunday evening, but there are concerns the exemptions leave holes in the system where the virus could come in.

From midnight, all border workers will be tested regularly. It'll be once a week for workers at quarantine facilities and those who transport people to or from them. Workers at managed isolation facilities, at the ports of Auckland and Tauranga and at Auckland International Airport will be tested once a fortnight.

The airport employees to be tested include Customs workers, airport security, cooks, cleaners and baggage trolley handlers. But airline crew and anyone travelling as a groom with their horse is exempt from the testing rules.

Auckland University public health expert Professor Des Gorman said the new rules are a "very good idea", but can't make sense of the exemptions.

"I don't understand the exceptions for airline crews and grooms - the border's the border."

Air New Zealand said some air crews are tested while travelling, and it is consulting with experts and employees to find a testing regime that "aligns with international rosters and addresses existing multiple mandatory" testing requirements.

Epidemiologist Michael Baker said New Zealand's border is vulnerable to air crews importing COVID-19.

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"We depend on them to keep freight and passengers moving, but we also need a system of high level of assurance not bringing in this infection."

He added the elimination plan and the community are still under threat since it's not clear how the virus got in last month or who brought it.

"It doesn't affect our ability to control it, it does affect our ability to prevent it happening again, and that's why we have to be cautious and find every loophole and prevent that."

The borders were already pinpointed as a weakness. In June, the Government targeted them in a strict testing regime, and two months later, Newshub revealed that regime was failing - nearly two-thirds of border workers weren't tested. 

"We just have to hope and trust that this time they will do what they say because we need that," Prof Gorman said.

One big new border job while the old one isn't over.