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."
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.
"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.
