The Anti-Doping Agency of Kenya (ADAK) was formed in January 2015, but its laws only came into force in June this year after it was declared compliant of the WADA codes
But Adak's integrity was called into question when two Kenyan track and field officials were caught up in two separate doping scandals at the Rio Olympics and were sent home from the games.
"The officials who include Rodney Swigelaar, WADA's Africa office director and Tom May, a member of WADA's Education and Development will carry out the audit to find out if ADAK has been conducting the doping tests, and carrying out sensitisation and education among the athletes," a top ADAK official, who requested anonymity told AFP.
"It is a standard procedure by WADA to launch such audit campaigns within its affiliate national organisations."
Kenya was under scrutiny after 40 athletes were suspended for drug-related offences between 2012 and 2014, and the country was only removed from the WADA non-compliant list after the adopted legislation was deemed in line with the WADA code in June.
Three top officials of Athletics Kenya (AK) are currently under suspension over graft and anti-doping probe.