Valcke, the right-hand man of outgoing Fifa President Sepp Blatter, was immediately relieved of his duties on Thursday.
Valcke "has been put on leave and released from his duties effective immediately until further notice," said a Fifa statement.
"Further, Fifa has been made aware of a series of allegations involving the secretary general and has requested a formal investigation by the Fifa Ethics Committee."
The 54-year-old French official had already been forced to deny involvement in a $10-million payment to South Africa in the wake of corruption allegations that forced Blatter's resignation earlier this year.
The latest claims against Valcke related to allegations of involvement in a scam to sell World Cup tickets at vastly 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 tickets at the 2014 World Cup.
The contract was subsequently cancelled.
In a strongly worded statement issued by Valcke's US-based attorney, the official decried the allegations as false.
"Jérôme 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.
"As has been reported, Fifa entered into an agreement with Mr Alon's company, JB Sports Marketing," the statement said.
"That agreement and Fifa's subsequent business dealings with Mr Alon were vetted and approved by Fifa and its legal counsel."
Fifa have been embroiled in a major corruption scandal since the arrest of seven of its officials on May 27th attending a Fifa congress in Zurich to elect a new president.
They are among 14 people charged by US authorities over more than $150 million in bribes given for television and marketing deals.
Despite the arrests in May the election went ahead with Blatter winning a fifth mandate although the 79-year-old then announced he would be standing down with a new election scheduled for February.
Valcke came under scrutiny in recent months over what he knew about a $10 million payment from the South African FA to an account controlled by the then North and Central American (Concacaf) football chief Jack Warner through Fifa in 2008.
US investigators believe the money was a bribe in return for backing for South Africa getting the 2010 World Cup.
Fifa has insisted it only acted as an intermediary between South Africa and former Fifa vice-president Warner, who quit world football's governing body and his other functions in 2011 over other corruption allegations.
Valcke said he only knew about the payment because he receives all correspondence sent to Fifa but he did not authorize the transfer.
The French official has found himself under scrutiny during his Fifa career.
In 2006 he was forced to step down as the football body's director of marketing after a New York court judged he had lied by negotiating Fifa deals with Visa in breach of existing contracts with Mastercard.
Fifa was later fined $60 million over the case — but Valcke re-emerged unscathed several months later in June 2007 when he was installed as Secretary-General.