"We would have preferred this to be kept in place because it gives us valuable information about the arrival of new variants," Bunce said.
He said there was an "absolute conveyor belt of variants" appearing at the border and that after a period of time if they kept appearing, there would be "leakage".
The BQ.1 variant was one that UK epidemiologists had been watching, he said.
Bunce said there had not been any community cases of BQ.1 detected.
BA.5 was still the primary variant in New Zealand.
Bunce said ESR was constantly looking at what was happening overseas, if variants were more transmissible and if they were causing more severe disease.
Regular monitoring of subvariants was carried out through both whole genome sequencing and wastewater testing.
Rat tests at the border provided important information on what to expect in New Zealand.
If a more transmissible variant was detected overseas it would previously have been detected at the border here.
With the removal of border testing that was unlikely to happen, Bunce said.
Previously international travellers needed to complete Rat tests on the day they arrived in New Zealand or the day after, and again five or six days later.
Now arrivals are provided a Rat test and encouraged to test, but it is not a requirement.
"We have five pillars of testing - border testing, testing at hospital, community testing, wastewater testing and counting cases," Bunce said.
"With the border testing gone, we have lost one of those pillars and softened our surveillance."
Other experts agreed, saying the recent dismantling of the border testing system will leave them without vital information and early warnings on new variants.
University of Auckland microbiologist Siouxsie Wiles told RNZ it was doubtful only 94 people out of almost 70,000 travellers who arrived in New Zealand had Covid-19.
"I'm not a statistician, but that seems highly unlikely, versus a change in our protocol to require people to be tested," she told RNZ.
In the week before the removal of the protection framework that required incoming travellers to undergo a Rat test, there were 525 border cases.
This dropped to just 94 reported cases in the six days after the Rat test requirement was removed.
Rat tests at the border provided an early warning system of new variants entering New Zealand. Without this, Wiles said, variants would spread in the community before being noticed.
The Ministry of Health confirmed there were three sequenced cases of BQ.1 and said the list of new subvariants appearing within New Zealand was lengthy and growing.
"New Zealand currently has a high level of immunity, based on high vaccine uptake and widespread infection predominantly with BA.2 and BA.4/5 variants," a spokesman for the Ministry of Health said.
"So far, no Omicron subvariants are showing significant ability to escape immunity from previous Omicron infection or have demonstrated a change in severity of disease."
