The Asian Football Confederation says that deputy general secretary Windsor John has replaced suspended general secretary Alex Soosay while the governing body investigates corruption allegations.
Soosay is accused of asking another official to hide documents during a review of AFC practices under disgraced former president Mohamed bin Hammam three years ago.
The claims were made last week by a Malaysian newspaper, the Malay Mail.
"Asian Football Confederation General Secretary Dato' Alex Soosay was today suspended by the AFC following media allegations which have recently surfaced concerning a case in 2012," said a statement released on Wednesday.
"A video statement conducted as part of a FIFA investigation was passed to media recently and the AFC has now been able to verify its authenticity."
The Malay Mail reported that the video showed a conversation between AFC financial director Bryan Kuan Wee Hoong and FIFA investigator Michael John Pride in which Kuan refers to a discussion he had with Soosay in 2012.
Soosay, a former player with Malaysian state side Negeri Sembilan, denies any wrongdoing.
He has held the position of AFC general secretary since 2008. Deputy boss John, another Malaysian, joined the Kuala Lumpur-based organisation in 2011.