The Kenyan runner tested positive for the banned substance hydroklortiazid in March this year.
Hydroklortiazid can make it more difficult to detect other doping-classified substances during doping tests, as well as contribute to rapid weight loss. It is usually used for elevated blood pressure.
Chepngetich voluntarily agreed to a provisional suspension during the AIU's investigation in April.
"During the months that followed, the AIU continued its investigation and issued today an official indictment and imposed its own provisional suspension", says Brett Clothier, head of section for AIU, in a statement.
The case will now be investigated by a disciplinary committee.
Last year, Chepngetich set a new world record in the marathon with a time of 2.09.56 during the Chicago Marathon. She also won the marathon race at the World Championship 2019 in Qatar.