The investigatory chamber of FIFA's ethics committee, world football's in-house prosecutor, also asked for Valcke's temporary suspension to be extended for 45 days while FIFA's judges weigh evidence against the organisation's former second-in-command.
In a statement, FIFA prosecutors accused Valcke of violating "the general rules of conduct," including "duty of disclosure, cooperating and reporting conflict of interest," while "accepting gifts and other benefits", among other charges.
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Investigators also called for the 55-year-old Frenchman to pay a fine of 100,000 Swiss francs ($99,000, 92,000 euros).
Valcke's suspension followed allegations of involvement in a ticketing scam, in which he was accused of selling World Cup tickets on the black market at above their face value.
Valcke's lawyer issued a statement on his behalf blasting FIFA's investigators.
"The Investigatory Chamber of the FIFA Ethics Committee has chosen to ignore Jerome Valcke's exemplary conduct and extraordinary contributions during his long tenure as Secretary General," said Barry Berke in a statement.
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"Today's press release is nothing more than a self-serving public relations effort to wrongly attack Mr. Valcke in a desperate attempt to try to prove that FIFA can police itself.
"Mr. Valcke did absolutely nothing wrong as any independent and fair review of the facts would establish."
Valcke had previously been accused of being party to a potential $10-million (9.25-million-euros) bribe paid to former head of the North and Central America football governing body CONCACAF, Jack Warner.
Valcke's suspension was due to expire at midnight and judges in FIFA's adjudicatory chamber may approve an extension later Tuesday.
But even without that approval, Valcke will not return to work as he has also been banned indefinitely by FIFA's management, a penalty that is separate from the ethics committee suspension.
Valcke's link to alleged graft within world football goes back to 2006.
While serving as FIFA's marketing director, he was thrown out of the organisation over a scandal involving key sponsor Mastercard.
Valcke was found to have negotiated with MasterCard's rival VISA in violation of the former company's right of first negotiation, a mistake that cost FIFA $90 million in a settlement.
Six months later, FIFA president Sepp Blatter promoted Valcke to secretary general, and the two were reportedly close through much of the last decade.
Blatter, 79, has been banned from football for eight years and is the target of a criminal investigation by Switzerland's attorney general.
As part of their investigation, Swiss prosecutors reviewed Valcke's emails.
The allegations of involvement in a black market ticket scam came from emails sent to the British press by Israeli former professional footballer Benny Alon.
Valcke's potential downfall is the latest in world football, hit by an unprecedented series of scandals that have sparked demand for major reform across the globe.
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