Kinyua was also the Kenyan team leader at the world championships in Beijing in August.
Okeyo has denied any wrongdoing, saying all funds have been fully accounted for by Athletics Kenya.
It's the latest blow to global track and field, the IAAF ethics commission said the officials were stood down to protect the "interests of the integrity of the sport".
The commission added that the trio is banned from acting in any IAAF or Athletics Kenya role pending investigation of complaints made against them.
The first case under investigation concerns the "potential subversion of the anti-doping control process in Kenya", the IAAF said. The second case involves accusations of "potential improper diversion from Athletics Kenya of funds received from Nike".
The IAAF said there was also a prima facie case involving "an apparent gift of two motor vehicles" from the Qatar Association of Athletics Federation in the period 2014-2015", which may have been received by Kiplagat personally or by Athletics Kenya.
In November 2014 Qatar was named the surprise host city of the 2019 World Athletics Championships.
The IAAF has already suspended Russia from all competition after a report commissioned by the World Anti-Doping Agency alleged Moscow had been involved in state-sponsored doping.