In the largest observational study of its kind, a review of Medicare records found that men treated with proton beams had one-third more bowel problems than those who had conventional radiation.
But there were also fewer complications in the months immediately after treatment.
According to Dr. Ronald Chen, a radiation specialist at the University of North Carolina, Chapel Hill, there is no clear evidence supporting proton therapy as a better option for prostate cancer treatment, and the new results suggest proton therapy could be more problematic.
Proton therapy uses proton particles instead of X-rays, targeting radiation more directly to tumors and sparing healthy tissue, which should lead to fewer side effects. Its value is established for treating eye and certain pediatric tumors. But it often is marketed for prostate cancer - a far more common condition.
Researchers said much more study is needed, but many hospitals are already adding proton centers as demand for the treatment grows. Proton therapy costs around $48,000, at least twice as much as other prostate radiation treatments.
The Associated Press contributed to this report.