The 32-year-old, who is also the reigning London Marathon champion, tested positive for the banned blood booster EPO in a test by the International Association of Athletics Federations (IAAF) in her native Kenya.
"The IAAF can confirm that an anti-doping rule violation case concerning the athlete Jemima Jelagat Sumgong (Kenya) has commenced this week," the IAAF said. "The athlete tested positive for EPO following a no-notice test conducted by the IAAF in Kenya.
"This was part of an enhanced IAAF out-of-competition testing programme dedicated to elite marathon runners which is supported by the Abbott World Marathon Majors group. The IAAF will make no further statement about this case until its conclusion."
Erythropoietin (EPO) is a natural hormone that stimulates red cell production. For a runner, injecting an artificially produced version increases oxygen absorption which allows them to run harder and faster without tiring.
Sumgong, who also tested positive for a banned substance in 2012, starred at the London Marathon last year, defying the odds to win despite suffering a bruising fall.
Steeled by her success in London, she then became the first Kenyan woman to win Olympic marathon gold, defeating Ethiopia's world champion Mare Dibaba in Rio to confirm her status as the world's top marathon runner of 2016.
Before news of her positive drugs test emerged, Sumgong had vowed to defend her London title on April 23. London Marathon organisers said they were "extremely disappointed" at Sumgong's failed test.
"She is currently suspended from competition pending the B test and the outcome of the investigation. Sumgong will therefore not run in London on 23 April to defend the title she won last year," announced the race's chief executive Nick Bitel.
He said that "athletes who are banned for a doping offence are banned for life from the event".
At the Rio Olympics, Sumgong defied temperatures of 28 degrees Celsius (82F) to claim an historic gold medal in a race that finished at the city's famed Sambodromo.
The athlete has not spoken out since the news of her failed doping test, however she posted a Bible verse on her Facebook page which said "do not be anxious about anything..."
Athletics Kenya said that if it was true that Sumgong had failed the dope test it was "extremely shocking and disappointing" to the whole nation.
In a statement the body said that it had worked "tirelessly to put in place measures to fight and eradicate the use and abuse of prohibited substances."
Earlier this year, Sumgong was one of a number of top Kenyan athletes who welcomed a new initiative to eradicate doping, which has tarnished their image, agreeing to be monitored by doctors appointed by the IAAF and Athletics Kenya.
"It will be easy for us now to communicate with these doctors before we take any medicine when the need arises," said Sumgong.
The move came after an investigation by German television channel ARD and Britain's Sunday Times newspaper last July alleging that doping was rife at the elite training centre in Iten.
Kenyan athletics boss chief Jackson Tuwei has warned that any athlete who failed to comply would not be selected to represent the country in international competitions.
"Forty-nine athletes have been found to have violated the WADA (World Anti-Doping Agency) code in the past five years but were cautioned according to the laws of the land and WADA code," said Tuwei.
Sumgong's former training partner, the 2014 Chicago and Boston Marathon champion Rita Jeptoo, is serving a four-year ban after also testing positive for EPO.
News of Sumgong's test was welcomed by other athletes. US distance runner Emma Coburn, a bronze medallist in the 3,000m steeplechase at last year's Olympics, applauded the IAAF's out-of-competition testing.
Out of competition testing is so important!! Well done, IAAF. I hope to see more productive results from no-notice out of competition tests https://t.co/G8Po8dSCNe
In 2012 Sumgong tested positive for steroid Prednisolone following the Boston marathon. She only served half of a two year ban after a successful appeal blamed the failed control on treatment for a hip injury.