"We should now plan on pandemics of the Covid-19 intensity occurring," the University of Otago epidemiologist said.
He said some governments or failed states could use biowarfare out of desperation.
"There are so many ways we have to prepare for bioterrorism threats."
He said Ebola was unlikely to be a threat in New Zealand but apart from Covid-19, two other coronaviruses had spilled over from animal reservoirs in recent years.
He said many crossover events, possibly thousands every year, happened when an animal virus infected a human. But often the person's immune response destroyed the incursion and no human-to-human transmission happened.
"A lot of virologists work very hard to predict these events but it's hard to predict them."
Sars was identified in 2002 and Middle East respiratory syndrome was identified a decade later.
Spillover infectious diseases from wildlife hosts to humans were becoming more frequent and severe, the Centre for Global Development nonprofit think tank said in an August study.
"Pandemic risk is largely under-estimated and actions to prepare for outbreaks are grossly under-invested," the CGD added.
In December, the Global Health Security Index found most countries, even wealthy ones, had not made dedicated financial investments in strengthening pandemic preparedness.
"Although many countries were able to quickly develop capacities to address Covid-19, all countries remain dangerously unprepared for meeting future epidemic and pandemic threats," the index added.
But there is good news.
Professor Dame Sarah Gilbert, creator of the Oxford/AstraZeneca vaccine, told the University of Oxford how rapidly scientists and others could work to combat new viruses.
"We were able to go fast in 2020 not because we cut corners or took risks with our product. We did every single thing that needed to be done," Gilbert said in a December lecture.
"We went faster because, when we had to, it turned out we could. "
Baker also said reasons existed to be hopeful, especially since so much work had been done battling Covid-19.
"All of the infrastructure we've built up now will be useful if we get a pandemic."
New Zealand has so far experienced far fewer deaths per capita from Covid-19 than many other nations.
"We're world leaders in rolling out and articulating elimination strategies," Baker said.
"There is a silver lining in the pandemic response."
Physical distancing and quarantine measures were likely to be deployed against future pandemics in similar ways to their use against Covid-19, he said.
"We can't undo the health and economic harm of the Covid-19 catastrophe but we can, we are, really obliged to learn from it."