Last week, AFC president Mohamed bin Hammam rejected FIFA´s instruction to reinstate the voting rights of Kuwait, Laos, East Timor, Afghanistan and Mongolia.
"If the issue of voting rights is not resolved, the members could quit," Velappan, who was the AFC´s secretary-general for 30 years, told reporters.
"The five countries barred from voting could immediately resign and if a number of other countries follow suit, disgusted by Hammam´s dictatorial style of leadership, we may have a major AFC split," he added.
Whether they vote or not will be decided at an AFC executive committee meeting on Thursday.
A day later, the AFC´s 46 member nations are scheduled to decide whether Bin Hammam keeps his FIFA executive committee seat or it goes to Bahrain Football Association president Sheikh Salman bin Ebrahim Al Khalifa.
Bin Hammam has vowed to step down from the AFC´s top job if he is ousted from his FIFA position.
Velappan said that a split among the grouping could see FIFA suspend the AFC, the world´s largest confederation.
"Among the consequences, FIFA could suspend recognition of the AFC and call on the Asian association to convene an extraordinary meeting to elect a new confederation," he said.
Velappan added that his dislike for Bin Hammam began after the Qatari suggested that AFC House be shifted out of Malaysia.
"One day I read in the newspaper that the AFC House was in danger of moving out of Kuala Lumpur. It was a house of joy when I left (in 2007). Today it is a house of terror and fear. After that I became very bitter with him," he said.
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