Jeptoo is a three-time winner of the Boston Marathon and two-time winner in Chicago. She is one of the highest profile Kenyan athletes to fail a doping test.
Tests of the "B'' sample were conducted between Wednesday and Friday at the World Anti-Doping Agency lab in Lausanne, Athletics Kenya said. The federation said in a statement that it will hold a hearing of Jeptoo's case early January.
David Okeyo and Jackson Tuwei, who are vice-presidents of Athletics Kenya, had said in November that Jeptoo's "A'' sample taken in an out-of-competition test in Kenya on Sept. 25 showed traces of the blood-booster EPO.
The 33-year-old Jeptoo claimed her second straight title in Chicago on Oct. 12. She was set to be crowned winner of the World Marathon Majors series before it was revealed that she had failed a doping test.
Earlier Friday the head of Kenya's athletics federation had said the doping problem in his country is far less severe than in Russia or China.
Athletics Kenya President Isaiah Kiplagat said the federation has banned or suspended 32 athletes for doping in the past five years.
"If you compare that to athletes banned by other federations like Russia and China, we are nowhere," he said.
Athletics Kenya has done all it could to "arrest "the doping problem, Kiplagat said.
Kiplagat's comments came as the World Anti-Doping Agency investigates allegations of systematic doping in Russia. Germany's ARD network alleged a web of doping, corruption and coverups in Russian athletics that implicated government-backed agencies.
Kiplagat said a Kenyan government taskforce will formulate laws to punish anyone found guilty of supplying Kenyan athletes with performance-enhancing drugs.
In 2012, ARD alleged there was widespread doping among Kenya's outstanding distance runners, saying the blood-boosting drug EPO and other prohibited substances were easily available from pharmacies in its high-altitude training camps.
WADA said in October it would work with Kenya to set up a national anti-doping agency.