The Kenyan runner set the world record by almost two minutes at the Chicago Marathon last October in 2 hours, 9 minutes, 56 seconds. It was her third win in Chicago.
She also won the marathon at the 2019 world championships in Qatar, where the women's race started at midnight to avoid extreme daytime heat.
The AIU gave no timetable for a disciplinary case for the 30-year-old runner.
Chepngetich was interviewed in person in Kenya in April and “complied with requests regarding our investigation,” AIU official Brett Clothier said in a statement.
The substance Chepngetich tested positive for, hydrochlorothiazide or HCTZ, can be used to disguise the use of performance-enhancing drugs.
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