Soosay was suspended on Wednesday after he allegedly asked for financial documents to be hidden prior to a probe of the AFC in 2012. He also been accused of embezzlement and theft.
"There should be an independent professional investigation into this… it’s in the interests of everybody to do that," Velappan told the AFP via telephone in Kuala Lumpur. "I personally feel very concerned with this situation and I think the AFC is obliged to really order an independent investigation and take all those to task if they have done anything wrong."
The allegations against Soosay came from the AFC's financial director Bryan Kuan Wee Hong, who gave videotaped testimony to a FIFA investigator in July 2012.
Hong told the investigator that Soosay had asked him to "tamper [with] or hide" potentially incriminating documents as the AFC were being investigated for financial wrongdoings under former president Mohammad Bin Hammam, who has been banned from football.
While there is a lot of evidence stacked against Soosay, Velappan called on current AFC president Shaikh Salman Bin Ebrahim Al Khalifa to launch a fair and professional investigation into the matter.
"I hope the AFC will conduct a really good, professional investigation into all this and if there’s anything [against] any of these top officials that appropriate action will be taken," he said. "We have got to protect integrity, we have got to protect good governance."
But, Velappan also admitted that the former Malaysia midfielder has some explaining to do.
"He has to explain…if you’re not guilty you don’t go to a guy [the AFC financial director] and tell him all these thing," he said.