Just hours after the 79-year-old chief announced his resignation - four days after being re-elected for a fifth term - a report in The New York Times claims that Blatter is now the subject of a corruption inquiry.
This morning Interpol issued a red notice for two former Fifa officials and four corporate executives for charges including "racketeering, conspiracy and corruption".
This comes as South Africa's Minister of Sport and Recreation, Fikile Mbalula, denied there had been any suggestion that his country had bribed officials in order to host the 2010 World Cup.
Former Fifa vice president, Jack Warner, and former Fifa executive committee member Nicolás Leoz, are among those on the wanted list.
Interpol's website states that it "seeks the location and arrest of wanted persons with a view to extradition or similar lawful action".
A red notice is not an international arrest warrant, and Interpol cannot compel any member country to arrest the subject of a red notice.
Warner, 72, handed himself in to police in Trinidad and Tobago last Wednesday but was released after paying $400,000 in bail. He has maintained his innocence.
Leoz, 86, was placed under house arrest in Paraguay on Monday.
Despite Blatter's attempts to distance himself from the controversy, which led to a number of key Fifa officials being detained by authorities following raids in Zurich last week, the FBI's attention is now focused on the outgoing president, The NYT reports.
Sepp Blatter is reportedly the subject of an FBI investigation
The paper states: "Several United States officials, speaking on the condition of anonymity, said that in their efforts to build a case against Mr. Blatter, they were hoping to win the cooperation of some of the Fifa officials now under indictment and work their way up the organisation."
Neither the FBI nor Blatter have commented on the report.
Interpol has issued a red notice for:
- Jack Warner, Trinidad and Tobago national, former Fifa vice president and executive committee member, CONCACAF president, CFU president and Trinidad and Tobago Football Federation (TTFF) special adviser.
- Nicolás Leoz, Paraguayan national, former Fifa executive committee member and CONMEBOL president.
- Alejandro Burzaco, Argentine national, controlling principal of Torneos y Competencias S.A., a sports marketing business based in Argentina, and its affiliates.
- Hugo Jinkis and Mariano Jinkis, Argentine nationals, controlling principals of Full Play Group S.A., a sports marketing business based in Argentina, and its affiliates.
- José Margulies (also known as José Lazaro), Brazilian national, controlling principal of Valente Corp. and Somerton Ltd., broadcasting businesses.
Blatter was re-elected on Friday, despite days of controversy and speculation leading up to the vote.
But on Tuesday he announced that he would call a new congress "as rapidly as possible" to elect a successor.
His re-election came after Warner and five others were arrested alongside current vice-president Jeffrey Webb and charged with racketeering, wire fraud and money laundering conspiracies in connection with an alleged "24-year scheme to enrich themselves through the corruption of international soccer".
Blatter's announcement also follows news that Fifa admitted paying $10 million destined for the South Africa World Cup to an account controlled by Warner.
The payment followed a letter from the South African Football Association to Fifa secretary general Jerome Valcke.
Blatter had resisted calls for him to resign, saying on Friday: "Why would I step down? That would mean I recognise that I did wrong."
In his acceptance speech on Friday, Blatter said: “Fifa needs a profound restructuring.”
He added: “Although the members of Fifa have given me the new mandate, this mandate does not seem to be supported by everybody in the world of football.”
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Yet in a hastily-called press conference on Tuesday, Blatter announced his resignation. He declined to take any questions.
He said: "I have been reflecting deeply about my presidency and about the 40 years in which my life has been inextricably bound to Fifa and the great sport of football.
"I cherish Fifa more than anything and I want to do only what is best for Fifa and for football.
"I felt compelled to stand for re-election, as I believed that this was the best thing for the organisation. That election is over but Fifa’s challenges are not. Fifa needs a profound overhaul."
The election is to take place between December and March and Blatter will remain in position until then.
Uefa president Michel Platini, who led calls for Blatter to resign last week, and Prince Ali Bin Al Hussein, who stood against the Swiss in last week's election, are among the names who have been tipped to run.
Football pundits rejoiced following the announcement from Blatter that he will step down.
English FA Chairman Greg Dyke led celebrations with a stinging criticism of the global football administrator's tenure.
Dyke pictured voting in the Fifa presidential election on Friday
He said: "He’s stood down. He’s gone. Let’s celebrate… this is nothing to do with Mr Blatter being honourable, he hasn’t been honourable in years."
“It’s great for football worldwide. Fifa would never get sorted out while he was there and it is a deeply flawed - possibly corrupt - organisation.”
Dyke's sentiment was echoed by Gary Lineker, former England footballer and a fervent critics of Blatter's almost 17 year-long Fifa administration.
Lineker took to Twitter to voice his comments, complete with heavily-laden sarcasm.
Following Blatter's resignation, and the mounting pressure on Fifa to investigate high-profile allegations of corruption concerning the 2018 and 2022 World Cup bids due to take place in Russia and Qatar, speculation is beginning to grow surrounding whether those commitments will be honoured.
Dyke also weighed in on the future hosts' chances, adding: “Great news... If I was in Qatar today I wouldn't be feeling very confident."
Blatter announces Qatar as the 2022 World Cup hosts
But while many are wondering if seeing the back of Blatter will mean a re-run of the Cup bids, both of which England applied to host, there certainly appears to be little consensus on the contentious matter.
New Culture, Media and Sport Secretary John Whittingdale weighed into the debate, insisting on Tuesday evening that the 2018 competition should go ahead in Russia as planned unless any new evidence of corruption came to light.
He has, however, previously called for Qatar to be stripped of the 2022 World Cup.