FIFA's own ethics committee, headed by former Switzerland international forward Claudio Sulser, is carrying out an inquiry and is due to make a final ruling in mid-November.
"The problem stems from the fact that when it comes to taking decisions to eradicate corruption, these decisions are delegated to an internal organ - that is, a body that is also part of FIFA," Zen-Ruffinen told French-language Swiss television channel TSR.
"I think it is the biggest problem. If one wants to eliminate corruption from FIFA, as the International Olympic Committee (IOC) succeeded in doing itself when there was a problem surrounding the organisation of the Olympic Games, the mandate has to be given to an outside body."
Zen-Ruffinen was FIFA general secretary from 1998 until 2002 when he left after accusing president Sepp Blatter of mismanaging the organisation.
He spoke on Sunday four days after FIFA's ethics committee provisionally suspended executive committee members Amos Adamu of Nigeria and Tahiti's Reynald Temarii.
Both have denied wrongdoing and said they expect to be cleared.
Zen-Ruffinen became involved in the story himself when the Sunday Times newspaper posted a film of him talking to undercover reporters.
"I confirm it was me, but it should be placed in the context of what happened," said Zen-Ruffinen.
"It was a discussion in the framework of a contractual relationship, a discussion that was totally confidential, held in a place that was not accessible to other people."
Voting on the World Cup hosts is restricted to the members of FIFA's executive committee. The decision will be made on December 2.
FIFA is also investigating allegations that two unnamed candidates have broken the rules by acting in collusion.
England, Russia, Spain/Portugal and Belgium/Netherlands are bidding to host the 2018 World Cup while Japan, South Korea, Australia, United States and Qatar are candidates for 2022.
