Valcke was FIFA's general secretary for nearly a decade, working alongside the body's then-president Blatter, who has been banned for eight years over an ethics violation.
Valcke, 55, was himself facing a possible nine-year ban sought by FIFA investigators over his alleged role in a scheme to sell 2014 World Cup tickets on the black market.
In a statement, FIFA said his employment contract had been "terminated", even before a verdict in the ticket case was decided.
Valcke's US-based lawyer Barry Berke said his client "remains confident that he will be fully vindicated and history will recognise all of his contributions to the sport he loves".
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"(He) is proud of all that was accomplished for the game of football during his long tenure as Secretary General," Berke added in an email sent to AFP.
FIFA said that Markus Kattner will continue to serve as acting general secretary, the body's number two post.
US prosecutors allege that 64-year-old Honduran Hawit accepted and laundered hundreds of thousands of dollars in bribes as general secretary of the Honduran federation between 2008 and 2014.
Hawit entered a plea of not guilty through his lawyer. The defendant looked pale and ill, and stood slightly stooped in the federal court in Brooklyn, following the proceedings through a court-appointed interpreter.
The Honduran will appear in court again on Thursday where conditions for bail will be discussed.
FIFA first suspended Valcke on September 17, when ethics committee investigators began probing the ticketing scheme. The suspension was renewed on January 6.
Valcke has also been linked to a $10 million payment made
by South Africa to corruption-tainted former Caribbean football chief Jack Warner.
US investigators reportedly believe this was a bribe to secure votes for the 2010 World Cup. But Valcke had been a controversial figure even before he was tipped as general secretary.
A New York judge said Valcke had lied to both companies. He was sacked as marketing director, but after the compensation deal, Blatter reappointed him as his deputy.
Blatter was banned by FIFA judges last month over a two million Swiss francs ($2 million, 1.8 million euros) payment to FIFA vice president Michel Platini, also the president of UEFA.
Switzerland is also investigating the attribution of the 2018 and 2022 World Cups to Russia and Qatar respectively.
The US justice department has charged 39 people and two companies with tens of millions of dollars worth of graft and bribery going back decades.
With the organisation currently being led by acting president Issa Hayatou -- a 69-year-old Cameroonian who has also been linked to corruption -- momentum is building towards a February 26 election where a new president will be chosen.