The substance, a diuretic, was detected in a sample collected from the Kenyan athlete on March 14th, the AIU said in a statement on Thursday.
"Chepngetich was not provisionally suspended by the AIU at the time of notification, however, on April 19th, she opted for a voluntary provisional suspension while the AIU's investigation was ongoing," said AIU Head Brett Clothier.
"In the intervening months, the AIU continued its investigation and today issued a Notice of Charge and imposed its own provisional suspension."
The AIU said HCTZ is used clinically to treat fluid retention and hypertension, adding that diuretics may be abused to mask the presence in urine of other prohibited substances.
Chepngetich smashed the women's marathon record in Chicago last October, running two hours, nine minutes and 56 seconds to become the first woman to break 2:10.
In April, Chepngetich withdrew from the London Marathon, saying at the time she was "not in the right place mentally or physically" to race her best.