Britain's Sunday Times and local Kenyan newspapers alleged Athletics Kenya (AK) vice president David Okeyo and two other senior federation officials made personal withdrawals from an AK account in which Nike deposited sponsorship money.
Kenyan police have questioned all three officials in relation to the withdrawals and on Sunday world governing body, The International Association of Athletics Federations (IAAF), said it had referred Okeyo to its ethics committee.
Okeyo said in a statement there was "no embezzlement of funds" whatsoever on his part.
"The funds are fully accounted for by Athletics Kenya and approved by the Annual General Meeting having gone through auditing process," he said.
Okeyo added that the deal with Nike was transparent and denied any cash was missing.
"I have noted various stories that have run in the media and are trending in the social media on the Nike/Athletics Kenya contract. I wish to state that the said contract was above board and was executed with integrity," he said.
Okeyo said he was waiting for investigations to finish and did not wish to comment further in the media.
Police have said Okeyo and two other AK officials recorded statements with the Kenyan Directorate of Criminal Investigations over cash withdrawals by the three on various dates as far back as 2011.
The IAAF informed its Ethics Commission about accusations against Okeyo this weekend when the Sunday Times cited court documents from a whistle-blower. Kenyan media made near-identical allegations at the start of the year.
"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 IAAF said in a statement.
"As part of the root and branch governance reform project that (IAAF president) 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 only duly vetted and declared as fit and proper persons to hold office."
(Writing by George Obulutsa; Editing by Ken Ferris)
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