Walking to work was also linked to a lower chance of being overweight or having raised BP, the survey of 20,458 UK adults found.
The researchers from Imperial College London said investing in alternative routes to work could significantly improve public health.
The study, published in the American Journal of Preventive Medicine, examined data from the Understanding Society survey conducted in 2009-11.
Almost one in five (19%) working age adults who used private transport such as cars, motorbikes or taxis to get to work were obese.
Cycling, walking, and taking public transport were all linked to a lower risk of being overweight than those who drove or took a taxi.
People who walked to work were 40% less likely to have diabetes than those who drove, while cyclists had a 50% lower risk.
Walkers were also 17% less likely than people who drove to have hypertension, although people who took public transport faced a greater risk than drivers.
Study author Anthony Laverty from Imperial College London said: 'The variations between regions suggest that infrastructure and investment in public transport, walking and cycling can play a large role in encouraging healthy lives, and that encouraging people out of the car can be good for them as well as the environment.'