The runners from a nation famed for its middle and long-distance runners were targeted in pre-competition tests at their team hotel in Beijing on Aug.
20 and 21, the IAAF said in a statement.
The East African nation’s sports body Athletics Kenya, which has been criticised by some of its own athletes for not taking the issue of doping seriously enough, said it had been told about the failed tests and had launched an investigation.
“Appropriate follow-up action will be taken in Kenya,” it said in a statement, adding that the two athletes had accepted their provisional suspensions.
“Athletics Kenya will provide full support and cooperation to the IAAF during the results management process,” it said.
The IAAF has spent the last month defending itself against accusations that it is soft on doping after data from thousands of blood samples were leaked to the media.
While critics of the IAAF might point to the positive tests as further evidence of widespread doping in the sport, the governing body is likely to see this as proof that their targeted testing is effective in weeding out drug cheats.
Zakary, 29, ran a Kenyan record of 50.71 seconds in the heat of the 400 metres in Beijing but failed to start the semi-final.
At Kenya’s national championships last month, Zakary had wowed athletics fans when she broke a 31-year-old national record held by compatriot Rose Waithera since the 1984 Olympics.
Manunga, 21, finished sixth in her heat in the 400 hurdles last Sunday and failed to progress to the next round.
Ahead of the Beijing championships, Britain’s Sunday Times newspaper and German broadcaster ARD/WDR reported they had been leaked suspicious blood results from more than 800 athletes, including 77 Kenyans.
In the last three years, 33 Kenyans have failed drugs tests but only Rita Jeptoo, winner of the Boston and Chicago Marathons, can be classed as a top runner.
Her two-year ban in January shocked Kenyans as it showed doping had risen to the top of the sport.
(Reporting by Nick Mulvenney in Beijing and Drazen Jorgic in Nairobi; Editing by John O’Brien, Amlan Chakraborty and Edmund Blair)