ABC News' Dr. Raheleh Sarbaziha reports:

The fish oil supplements that millions of American men take each day to cut their risk of heart disease might have a dark side, at least according to a study released today that is sure to generate controversy.

Can fish oil really prevent heart disease?

The new study, published today in the Journal of the National Cancer Institute, suggests that men who have higher levels of omega-3 fatty acids in their system face a 43 percent increased risk of developing prostate cancer and a 71 percent increased risk of the high-grade form of the disease.

To determine this, the researchers relied on data from a past study that examined the blood concentrations of omega-3 polyunsaturated fatty acids in 834 men with prostate cancer and 1,393 men without prostate cancer. When they did this, these researchers found an association between high omega-3 levels and the occurrence of prostate cancer.

Read about the effects of fish oil on breast cancer risk.

Whether the increased level of omega-3 in the men with prostate cancer was from supplements or from oily fish in their diet was unclear. But lead study author Dr. Theodore Brasky of Ohio State University Comprehensive Cancer Center said that no matter the source, the findings suggest that men should be wary of getting too much of the nutrient.

"Men will probably want to talk to their doctors, especially those patients who have been recommended increased fish oil intake," Brasky said. "They should probably moderate their intake of fatty fish and they should avoid fish oil supplements at this time, especially considering that when men are taking fish oil supplementation they are taking [higher doses than they need]."

But some experts say more evidence is needed before men make drastic changes. ABC News Chief Health and Medical Editor Dr. Richard Besser said that the original study from which this data was drawn was not specifically designed to look at the exact relationship between omega-3 fatty acid intake and prostate cancer, so men should think twice before discontinuing them entirely.

"This is not proof that omega 3's cause prostate cancer," he said.

If anything, Besser added, the finding should reinforce the notion that better dietary health does not necessarily come in a pill form.

"If you want omega 3's, get them from food," he said. "The more we look at supplements, the more untoward consequences we find."

Read about the dangers of mixing supplements with medications.

Doctor's Take

So where does this leave men who, based on this study, are worried that they will have to choose between a healthy heart and a healthy prostate?

The first thing that these men should do is speak to their doctors prior to making any changes to their diets and discontinuing current supplementation. In particular, men with active heart conditions or elevated cholesterol levels should approach their cardiologists and discuss the risk versus the benefits of consuming fatty fish and fish oil supplementation.