A source close to FIFA said the 63-year-old - a member of the executive since 2011 - was banned while Michael Garcia, the chairman of the investigatory chamber of the ethics committee, examines an alleged misuse of Asian Football Confederation funds.
Fernando was a close ally of former FIFA executive committee member and AFC president Mohamed Bin Hammam, who was banned from football for life by FIFA following his involvement in the 2011 bribery scandal when he was standing against Blatter for president.
Bin Hammam was due to stand against Blatter in the election but pulled out after it was alleged he tried to bribe Caribbean delegates.
Fernando accompanied Bin Hammam on his ill-fated trip to Trinidad which precipitated the Qatari's downfall.
Despite his initial ban being annulled by the Court of Arbitration for Sport, Bin Hammam resigned from all his football-related responsibilities in December after being charged with repeated violations while president of the AFC.
He was again banned for life by FIFA.
Fernando lists his profession as an attorney at law on FIFA's executive committee web page, says his hobby is "playing the stock market" and states his fondest footballing memories are meeting Pele and "being elected at FIFA".
However, his ban means he will not take part in the next FIFA executive committee meeting next week and cannot play any part in the political manoeuvring that is building ahead of the Asian Football Confederation presidential elections in Kuala Lumpur on May 2.
Those elections will end a difficult period in the governance of Asian football with a permanent successor to Bin Hammam finally appointed.
Blatter, who has vigorously denied media accusations regarding his own probity over the last few years, approved the establishment of an independent investigation into world football's governing body with the aim of ridding it of dishonest officials and the suspicion that the body was corrupt.
Nigerian Amos Adamu and Reynald Temarii of Tahiti, at the time the president of the Oceania confederation, were banned for their part in a cash-for-votes scandal involving voting for the World Cup after being trapped by an undercover investigation by the Sunday Times newspaper in London.
In the recent past a number of high profile officials have left the executive committee, including Jack Warner of Trinidad and Tobago, Bin Hammam, Ricardo Teixeira of Brazil and Chuck Blazer of the United States.
Although FIFA will not confirm why Fernando has been suspended, there are currently at least three on-going investigations being undertaken into FIFA, under the general umbrella of the Independent Governance Committee headed by Swiss lawyer Mark Pieth.
In its statement, FIFA said the decision to ban Fernando was taken "based on Article 83, Paragraph One of the FIFA Code of Ethics, in order to prevent interference with the establishment of the truth with respect to proceedings now in the adjudicatory chamber".