Okeyo, a member of the IAAF ruling council, is alleged, along with two other officials, to have syphoned off funds from a sponsorship deal between the national association and multinational sportswear giant Nike.
"An investigation by The Sunday Times and the German broadcaster ARD/WDR has uncovered a sworn affidavit in which a whistleblower claimed that the officials syphoned close to $700,000 (650,000 euros) out of the federation's bank account, most of it in cash. He says he reported his concerns to the police," the Sunday Times said.
The allegations came as news to the IAAF, whose newly-elected president Sebastian Coe has come in for intense criticism for retaining his role as an ambassador for Nike.
"The IAAF was not aware of the investigation into Mr Okeyo in Kenya and the information has immediately been passed on to the independent IAAF Ethics Commission," the International Association of Athletics Federations said in a statement.
"As part of the root and branch governance reform project that Sebastian Coe has announced, there will be new processes introduced to ensure all persons appointed to IAAF Commissions and advisory groups in the future have been duly vetted and declared as 'fit and proper persons' to hold office.
Okeyo denies any wrongdoing, but the investigation heaps further embarrassment on the IAAF, which on Friday provisionally suspended Russia from all competition after a report commissioned by the World Anti-Doping Agency (WADA) alleged the country had been involved in state-sponsored doping.
Former IAAF president Lamine Diack, his son Papa Massata Diack, advisor Habib Cisse and the former IAAF anti-doping chief Gabriel Dolle are all being investigated by French police over allegations they were complicit in covering up Russian doping, allegations they deny.
The spokesman added that Nike was co-operating with the local authorities in their investigation.
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