The Frenchman has also been accused of involvement in bribery. He has denied any wrongdoing.
FIFA investigators have called for a nine year ban from any football activity for Valcke along with a fine of 100,000 Swiss francs ($99,000/92,000 euros).
FIFA's ethics commmittee adjudicatory chamber said that following a report by the investigators it had decided to "institute formal proceedings" against Valcke.
The action follows allegations of involvement in a scheme in which Brazil World Cup tickets were sold on the black market.
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FIFA investigators have accused Valcke of failing in his duty of disclosure, failing to cooperate with the inquiry, conflicts of interest and offering and accepting gifts.
Valcke's US lawyer Barry Berke on Tuesday blasted the FIFA investigation, insisting Valcke "did absolutely nothing wrong."
"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," Berke added.