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Covid-19 was poorly controlled in Auckland, risks of outbreaks remained in the rest of New Zealand and vaccination rates were not yet high enough, he said.
"Level 1 — anywhere in New Zealand this year — must be in doubt," Prof Baker said.
His comments followed cases of community transmission emerging in Waikato yesterday and before Cabinet decides today if and how Auckland should remain in Level 3.
Disease modeller Prof Michael Plank, of the University of Canterbury, said moving Auckland down a level would be extremely risky and Prime Minister Jacinda Ardern has said other parts of the country would not drop to Level 1 while Auckland remained at Level 3.
The Government has reserved Level 1 for when the disease is contained.
Prof Baker suggested a more permissive Level 2 — such as allowing another increase in the number of people permitted to gather at indoor venues — might need to be considered soon for parts of New Zealand.
Possible approaches included differentiating between measures needed in the North Island and South Island and tightening the border around Auckland for several weeks.
Hamilton, Raglan and other Waikato towns moved to Level 3 last night after the discovery of two community cases of the Covid-19 Delta variant in the region.
The total number of community cases reported yesterday was 33 (32 in Auckland) and there were 27 community cases, all in Auckland, on Saturday.
One of the Waikato cases was to be added to the tally today.
Queenstown-Lakes Mayor Jim Boult said a likely extension of travel restrictions through the school holidays was worrying for businesses in the South that normally benefited from Auckland visitors. People were exhausted — physically, mentally and financially — from dealing with ramifications of the pandemic, he said.
"Businesses face shutting the doors," Mr Boult said.
Level 3 restrictions will apply in Waikato for an initial five days while contact tracing, testing and wastewater testing occurs.
Recent wastewater testing in Waikato had come back negative, Ms Ardern said.
A move back to Level 4 was not being considered for Auckland, she said.
Ms Ardern urged people to get vaccinated.
"It is not a coincidence that those in our current [Waikato] outbreak have not been vaccinated."
The two Waikato cases were connected to each other but not, at this stage, to Auckland's outbreak. Director-general of health Dr Ashley Bloomfield said further investigation, including genome sequencing, should help work out the link.
A Covid-positive truck driver who travelled to Palmerston North was included in yesterday’s case numbers. They were picked up through routine surveillance, Dr Bloomfield said.
Prof Baker said moving Auckland to Level 2 was already unlikely before taking into account the new Waikato cases.
A public health group Prof Baker belonged to called for an urgent meeting to review Covid-19 containment measures in Auckland.
Prof Plank said Level 3 would struggle to contain the outbreak there.
Covid-19 Response Minister Chris Hipkins said people aged 17 and over who were not New Zealand citizens would need to be fully vaccinated to enter the country from November 1.
They will need to have had a full course of any of the 22 vaccines approved by a government or approval authority.
The last dose would need to be at least 14 days before arrival.
A parent of a baby in the neonatal intensive care unit at Auckland City Hospital tested positive for Covid-19 yesterday, the Ministry of Health said.
In a statement last night, the ministry said it had been advised of the result by the Auckland DHB.
Movements in and out of the neonatal unit have been restricted and the DHB is testing all staff, whanau and babies in the unit as a precaution.
The DHB's initial investigations suggest the risk to babies in the unit is low, the statement said.
— With NZ Herald and RNZ