In Auckland, the researchers predicted 57 fewer premature deaths each year, and that carbon emissions from cars would be 20 per cent lower.
Tauranga and Hamilton would have 50-52 fewer premature deaths each year, and 27-32 per cent lower carbon emissions from cars.
Lead author Dr Caroline Shaw said this showed the clear benefits of sustainable transport.
She said Wellington's increased use was down to different urban planning decisions from local councils over recent decades.
"It's not like this is a hardship.
"Cities that have high levels of sustainable transport are nice cities to be in, they're nice cities to live in," she said.
"What we've seen in recent years is a real transformation of how we think about housing.
"We used to think of it as just a roof over our heads but now we know that housing's really important for health. It's somewhere warm, somewhere safe, somewhere that keeps you healthy. We need the same transformation for thinking about transport."
Shaw said the research showed the high cost of giving car infrastructure preferential treatment, when sustainable transport could be improving health and lowering carbon emissions.
"[Transport systems are] not just about moving trucks from one side of the city to another.
"They are about preventing depression and preventing cancer and preventing heart disease and making our cities places that we enjoy being in and of course contributing to saving our planet by reducing emissions."
Shaw said even Wellington was too dominated by cars, and had room for improvement.
The researchers used the Integrated Transport and Health Impacts model, developed in the UK and adapted to New Zealand, for their calculations.
The full research is published in the New Zealand Medical Journal this week.
