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."
Chepngetich's agent did not immediately respond to a request for comment from Reuters.
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.
Marathon running has been hit with a spate of high-profile doping cases in recent years, particularly from Kenya, which is world-renowned for its middle and long-distance runners.
In April 2023, Athletics Kenya said its government pledged $5 million per year for five years to fight doping in athletics.
In February 2024, Kenya's Sarah Chepchirchir was hit with an eight-year ban after the former Tokyo Marathon winner was found to have violated anti-doping regulations for a second time.
A year later, Kenyan marathon runner Brimin Kipkorir was also provisionally suspended by the AIU after he tested positive for prohibited substances.