She tested positive for hydrochlorothiazide, a diuretic, on Sunday, it said. On that day the 18-year-old took part in the women’s 100m butterfly final, finishing fourth.
Chen has applied to the International Olympic Committee for further tests and a hearing, it added.
Diuretics increase urination rates and can be used as “masking agents” to hide the presence of performance-enhancing substances that are screened for in doping tests.
China has already been embroiled in doping controversy in Rio after Australia’s Mack Horton called Sun Yang a “drugs cheat”, prompting a formal demand for an apology by Chinese officials.
Sun, China’s most successful swimmer, served a three-month doping ban in 2014, which was only announced retrospectively by Chinese authorities.
In March, the CSA revealed that six Chinese swimmers had tested positive for drugs in the preceding months, although two of them were only given warnings.