In September, the 24-year-old four-time Olympic medallist’s urine sample was tested positive ahead of the Asian Games and the swimmer immediately blamed the injection he got in July at a hospital.
A spokesman for the prosecutors' office said the doctor was being charged with causing injury through negligence, the Yonhap news agency reported.
Park had asked the doctor before getting the injection if it contained any substances that could be a problem if he was tested, and was told there was no cause to worry.
According to the Chosun Ilbo daily, Park received the injection as part of an "anti-ageing" procedure he had been offered for free.
Park became the country's first Olympic swimming medallist when he won gold in the 400m freestyle and silver in the 200m freestyle at the 2008 Games in Beijing.
His positive dope test will be the subject of a FINA hearing on February 27 in Lausanne.