The 21-year-old Koki Manunga and the 29-year-old Joyce Zakary -- who are both 400 meter runners -- were provisionally suspended by the International Association of Athletic Federations (IAAF) after returning positive samples on August 20 and 21 respectively at the World Championships in Beijing, China.
"These targeted tests were conducted by the IAAF at the athlete hotels during the pre-competition phase," said an IAAF statement.
"The IAAF will not discuss the details of the cases as they progress through the results management process."
As it launched its own investigation, Athletics Kenya (AK) said it had met with the IAAF and the two athletes.
"Athletics Kenya will provide full support and cooperation to the IAAF during the results management process and will not be providing further comment at this stage," the organization said in a statement sent to CNN.
Prior to the start of the World Championships the IAAF, which last week elected its new head -- British former Olympian Sebastian Coe -- has had to battle doping allegations.
Earlier this month, Britain's Sunday Times and German broadcaster ARD revealed they had access to a leaked database containing more than 12,000 blood tests from 5,000 athletes from 2001 to 2012. Leading experts concluded that these that these revealed an "extraordinary level of cheating" in the sport.
In response to those reports, AK said they were "an attempt to smear" its team ahead of the World Championships.
"AK has been at the forefront of identifying doping as a problem and in the past two years we have devoted a lot of time and resources to combat the vice with the assistance of IAAF, the World Anti-Doping Agency, the Kenyan government and international partners such as China and Norway," it said in a statement on August 2.
"We have committed resources on doping sensitisation of our athletes at annual seminars and our leaders have used every available platform to emphasize the dangers and perils of using banned substances.
"Our mission as a national federation in conjunction with our partners is to ensure a clean sport of athletics and therefore will do everything within our mandate to tackle the issues of doping."