They were also 60% less likely to develop an aggressive form which can spread to other parts of the body.
But charities say the evidence, reported in the Journal of the National Cancer Institute, is still unclear.
They do not recommend that men take up coffee drinking in the hope of preventing prostate cancer.
Unknown compounds The study looked at about 48,000 men in the US who work as health professionals.
Every four years between 1986 and 2006, they were asked to report their average daily intake of coffee.
During this 20-year period, 5,035 of the men were diagnosed with prostate cancer, including 642 fatal cases. Each year about 37,000 men are diagnosed with prostate cancer in the UK
- Some 10,000 die from the disease
- Symptoms include problems passing urine but they may be mild or non-existent
No difference was seen between caffeinated and decaffeinated coffee, suggesting caffeine itself was not the cause.But even relatively small amounts of coffee - one to three cups per day - were found to lower the risk of lethal prostate cancer by 30%.
The researchers think there may be unknown compounds in coffee that protect against the disease.
Lead researcher Dr Kathryn Wilson, from the Harvard School of Public Health in Boston, said: "At present we lack an understanding of risk factors that can be changed or controlled to lower the risk of lethal prostate cancer.
"If our findings are validated, coffee could represent one modifiable factor that may lower the risk of developing the most harmful form of prostate cancer."
Commenting on the study, Dr Helen Rippon of The Prostate Cancer Charity, said other studies had not shown the link and the research evidence was still unclear.
She added: "Although this study is a welcome addition to our knowledge, it is far from definitive and we would not recommend men who are not already habitual coffee drinkers to become so in the hope of preventing prostate cancer.
- Previous studies have shown no clear link between coffee and prostate cancer risk
- Men who drank six or more cups of coffee per day had a slightly lower risk of any form of prostate cancer and a substantially lower risk of lethal prostate cancer compared with non-coffee drinkers, according to the researchers
- Both caff and decaff were associated with similar risks
"Heavy caffeine intake is associated with other health problems and men with benign prostate problems might well make urinary symptoms worse."Yinka Ebo, senior health information officer at Cancer Research UK, said: "There's no need for men to start drinking gallons of coffee in an attempt to lower their prostate cancer risk.
"A number of other studies looking at coffee and prostate cancer have found that drinking coffee does not affect the risk of the disease, and this study only found a lower risk of advanced prostate cancer in men who drank more than six cups a day.
"We would need to see these results repeated in other large studies before we can be sure whether coffee consumption affects the risk of prostate cancer."