"If you have at the moment maybe 100 people a day arriving with this virus, and potentially seeding across the country, that becomes one of the factors that sustain transmission in New Zealand and the source of new variants," Baker said.
"I think we need to look at whether we should have a vaccination requirement for travellers, whether we should use testing technology, which is now getting very effective, as part of the arrival process into New Zealand," he said.
"There's a lot of things we can do, and I think we shouldn't just abandon all controls at the borders."
With New Zealand fully reopening its borders and removing restrictions, it was likely that new variants that emerged overseas would appear here "quite rapidly", he said.
"So [it's] another reason I think we just need to look very hard at our surveillance systems.
"The whole genome sequencing now is a great tool, but it does depend on the ability to sample people who are infected and that has now dropped that ability because there will be fewer testing of people in New Zealand because of the loosening of testing requirements."
Baker believed there needed to be a successor to the traffic light and alert level systems in preparation for the current pandemic's next challenges and because "the evidence is that pandemics, unfortunately, are becoming more common at the moment".
"We should be planning for having a potential rise in cases at some point in the next six months.
"And so that's why my main concern with the change is that we're not retaining some kind of way of categorising the level of risk and having a proportional response.
"We know from the history of this virus is it's going to produce or it's very likely to produce new variants that will drive more waves and we're going to have waning immunity."
During yesterday's announcement, Prime Minister Jacinda Ardern acknowledged it would be important to monitor variants, adding that targeted surveillance, including wastewater testing, would be used at the border.
"We will continue to offer follow-up PCR tests and genome sequencing of positive cases among travellers."
Covid-19 Minister Ayesha Verrall also said the Government would continue to monitor testing and the international situation and would maintain preparedness for variants.
The Government was also ensuring public service chief executives' roles and responsibilities were clear should a pandemic response be needed again in future, Verrall said.
She told Nine to Noon the risk had changed compared with earlier in the pandemic or even earlier this year.
"Cases are a 10th of what they were earlier in the year, pressure on the health system has substantially reduced in terms of Covid, the protections that are alternatives to the restrictions are substantial, including the high vaccination rates that we have, the levels of hybrid immunity because of some natural infection and as well the protections we have in the health system including access to antiviral medication."
Modelling, which now takes into account some of that hybrid immunity, suggested a "very limited" increase in risk from the removal of mandates, she said.
Waning hybrid immunity may give rise to a small bump in community case numbers, but this might be less than what seen already this year, she said.
Vaccination requirements for health workers
All Government vaccine mandates are set to end in two weeks on September 26 - any vaccine requirements would be at the discretion of employers.
Baker said this was problematic for the health system in particular and its workers.
"It's an occupational health and safety requirement that we should look after all our workers, and we know health care workers have been very vulnerable during the pandemic," he said.
"I think we have to look at the wider vaccination requirements like flu vaccines for health care workers. The pandemic has, I think, shone a light on the fact that this is an area of vulnerability for the health system, for the workers themselves, and for their patients.
"And also I think just the integrity of the system, that it's hard to advise your patients to be vaccinated if you're not vaccinated yourself."
Ardern told Morning Report the Government had always reiterated it did not want to keep mandates for longer than the evidence suggested it was needed.
