New Zealand was put in lockdown on Tuesday after a man in Auckland tested positive for the highly infectious Delta variant.
The total number of cases in the current outbreak stands at 51, with cases in the country's largest city Auckland and the capital Wellington. The country is in a level 4 lockdown due to last until at least 11.59pm on Tuesday.
Cabinet will meet on Monday to decide on any extensions and/or lowering alert levels for parts of the country.
Professor Baker was speaking to Newstalk ZB this morning and said there were a huge number of exposure events, some of which could end up being "superspreaders", with large numbers of people infected.
"Given the huge number of exposure settings and that some of these were quite high-risk indoor environments, we are obviously expecting quite a few more cases," Baker, an epidemiologist at the University of Otago's Wellington campus said.
"The good news is that these infected cases were only in the community for a short period of time, because we do know when the virus first arrived in New Zealand ... that really is good news because it limits how many times the virus will go through its reproduction cycle, and we know that each case on average may infect five or six others, but it only had 7 to 10 days in the community to go through those cycles. So it won't be a huge outbreak, fortunately."
The Delta variant is much more infectious but had a shorter incubation period, Baker said - around two, three or four days. That meant new cases should come through more quickly.
"We should see it peak very soon, actually - just this week."
While it could be unsettling to see more and more cases confirmed each day, Baker said New Zealanders should take heart in the fact Delta community outbreaks had been contained, including South Australia and Queensland.
The New Zealand Government had done the critical thing and imposed a strict lockdown soon after the first case was detected, he said.
"I am sure we will beat this."
An important factor in how quickly the outbreak could be contained would be how many people were infected after people with the virus attended indoor events like church services.
"I know when I looked at that growing list of places of interest ... my heart sank, because it included just about every high-risk indoor event you can think of. But, again, it just comes down to whether there was an infectious person at one of those events or not."
Baker was impressed by the levels of vaccination that had been sustained, despite the lockdown and need to also ramp up testing to record levels.
He thought the daily vaccination rate could improve even further, given there was no longer a supply problem.
Asked about weaknesses in our lockdown, Baker said New Zealand's was about the strictest in the world, but still had gaps. One was essential workers who were at higher risk. Another was young people with large social networks and who might be less inclined to follow the rules.
When asking people to observe the lockdown restrictions, Prime Minister Jacinda Ardern has often pointed to the ongoing Delta outbreak in New South Wales. Baker said elimination "may have" passed NSW by, and they could now be looking at a suppression strategy.
That was much tougher on the population, he said, with ongoing restrictions and more illness and death. Even in the United Kingdom, with high vaccination rates, there were still 800 people ending up in hospital with Covid-19 every day, and about 100 dying.
Baker said it was essential for New Zealand to continue with the elimination strategy until we had high vaccine coverage. By early next year a discussion would be needed about whether that strategy should be continued, he said, or switched to a suppression approach.
"I don't think we know enough yet about this virus to know what to choose."
