The AFC released a brief statement saying the Malaysian had been suspended while they investigate the media claims relating to a case dating back three years.
"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," the statement said.
The AFC said deputy general secretary Windsor John would replace Soosay on an interim basis while the investigation was carried out.
Soosay was accused by a Malaysian newspaper of ordering some documents to be hidden during a review of AFC practices under former president Mohamed bin Hammam, who was later banned for life by FIFA for corruption.
Soosay has denied any allegations of wrongdoing and told Reuters earlier this month that he believed the case was closed.
But the AFC said on Wednesday that he had been suspended after they had seen and verified a video that was part of the investigation.
"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 AFC said.
The allegations first surfaced last month when the Malay Mail newspaper published a report claiming Soosay had asked another AFC official to "protect me".
The newspaper said Soosay had made the request to AFC financial director Bryan Kuan Wee Hoong.
The Malay Mail said the video involved a conversation between Kuan and FIFA investigator Michael John Pride where the AFC official discussed a conversation he had with Soosay in 2012.
A former player, Soosay has held the position of AFC general secretary since 2008.
His role meant he worked closely with Qatari Bin Hammam, who was initially banned by football's governing body for bribery ahead of the 2011 FIFA presidential elections in which he was standing against incumbent Sepp Blatter.
Bin Hammam eventually overturned the verdict after a lengthy court process only to be banned following a review of AFC accounts by FIFA who accused him of repeated violations of the ethics code during 2008-2011.
(Reporting by Patrick Johnston; Editing by John O'Brien/Julian Linden)
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