Agent Federico Rosa told The Associated Press that Jeptoo tested positive in an out-of-competition test in Kenya in September. Athletics Kenya said later Friday that the test was on Sept. 25 — just over two weeks before the Chicago race — and that the athlete's "A'' sample "indicated the presence of prohibited substances."
The federation said it was "disappointed to announce that we have received communication from (world athletics body) IAAF" that Jeptoo failed a test.
Rosa and the federation declined to identify the substance or substances.
Athletics Kenya said its medical and anti-doping commission would meet with Jeptoo early next week to determine whether she wants to have her backup "B'' sample tested.
However, Rosa told the AP that the backup test was not required.
"We will legally go after the person or the people that convinced Rita to do this," Rosa said, adding Jeptoo's management had "nothing to do with" any doping.
"I am sorry for Rita," he said.
The IAAF said in a statement that it was "not in position where it can confirm or deny" Jeptoo's positive doping test.
"The case remains in the confidentiality phase," the IAAF said, "although that should be lifted within the next week."
The 33-year-old Jeptoo won the Chicago Marathon on Oct. 12 in 2 hours, 24 minutes, 35 seconds, her fourth straight major marathon victory. She has also won back-to-back titles at the Boston Marathon, where she set the course record on April 21 in 2:18:57.
Jeptoo currently leads the World Marathon Majors series, a two-year series that includes the biggest marathons in the world and culminates with Sunday's New York Marathon. Jeptoo was not scheduled to run in New York, but was still set to claim the $500,000 top prize.
The world marathon group said earlier Friday that it had postponed Sunday's awards ceremony because of the positive test.
"No athlete can win the World Marathon Majors Series title who has been in breach of IAAF anti-doping rules," the group said.
Jeptoo's failed test comes as Kenya is under close scrutiny for a recent spike in doping cases — particularly among its world-famous distance runners.
The World Anti-Doping said in October it would work with Kenya to set up a national anti-doping agency. A government-commissioned investigation was set up after German broadcaster ARD alleged in 2012 that there was widespread doping among the nation's distance runners.
"It shows that testing is being carried out," marathon world record holder and former world champion Paula Radcliffe said of Jeptoo's positive test. "Maybe at least this time it comes before the (World Marathon Majors) payment is made."
AP Sports Writer Rachel Cohen in New York contributed to this report.