Doctors Without Borders (MSF) randomly surveyed over 800 women between the ages 18 and 49 in the Rustenburg area, northwest of Johannesburg, over a two-month period at the end of 2015.
"What we found from the survey is that one in four women has been raped in Rustenburg," Garret Barnwell, an MSF humanitarian affairs officer in the area, told AFP.
"What was quite striking for us is that if you use the prevalence rate, you can say that there were round about 11,000 women who were affected every year," he added.
The report also showed that only five percent of the women who were raped visited a health care facility for post-rape care and treatment.
Stigma plays a part, said Barnwell, adding that respondents also had trouble trusting the staff at clinics.
"Survivors of sexual violence face numerous other barriers to seeking care -- stigma within communities is high, and options are few for accessing well-resourced, dedicated sexual violence health services," read the report.
Only half of those surveyed knew that HIV infection could be prevented by rapid use of anti-HIV medication after being raped.
MSF said the report results were "shocking but not uncommon" in a country where the prevalence of rape is generally high.
According to the latest crime statistics, 43,195 rapes were recorded across South Africa during the 2014/15 reporting period, the lowest figure in five years.
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