Valcke was put on indefinite leave on Thursday night over accusations that he agreed to let World Cup tickets be sold at a vastly inflated price.
The Frenchman strongly denied the allegations. But FIFA's chief of finance Markus Kattner took over "all duties" held by Valcke in the day-to-day running of football's governing body, FIFA said.
With FIFA still overshadowed by US and Swiss corruption investigations, it announced on Thursday night that Valcke "has been put on leave and released from his duties effective immediately until further notice."
FIFA said it had been "made aware of a series of allegations involving the secretary general and has requested a formal investigation by the FIFA Ethics Committee".
Valcke has been accused of involvement in a scam to sell World Cup tickets at inflated prices and take a slice of the profits.
The claims were made by Benny Alon, an American-Israeli consultant at a company which had a deal with FIFA to sell 2014 World Cup tickets. The contract was subsequently cancelled.
In a strongly-worded statement issued by Valcke's US-based attorney, the official decried the allegations as false.
"Jerome Valcke unequivocally denies the fabricated and outrageous accusations by Benny Alon of alleged wrongdoing in connection with the sale of World Cup tickets," the statement from New York attorney Barry Berke said.
The statement said Valcke "never received or agreed to accept any money or anything else of value from Mr Alon".
All dealings between Valcke and Alon's company had been cleared by FIFA's legal department, the statement added.
