The former Asian Football Confederation president was handed a lifetime ban from all football activity last year after being found guilty of bribery by a FIFA ethics committee panel during his campaign for the presidency of the sport's world governing body.
However, bin Hammam's ban was annulled by the Court of Arbitration for Sport on July 19 after his appeal was upheld on grounds of insufficient evidence.
The Qatari was provisionally suspended by FIFA's ethics committee following the CAS ruling and a statement from the body on Friday read: "The chairman of the investigatory chamber of the FIFA ethics committee, Michael J Garcia, today formally opened investigation proceedings against Mohamed bin Hammam.
"These proceedings follow the provisional banning of Bin Hammam for 90 days as established by the Ethics Committee on 26 July 2012 after a preliminary investigation of the case."
In response to FIFA's latest move, bin Hammam has pledged to clear his name in a letter to AFC committee members.
"My legal team has filed an immediate response to the actions of the AFC and FIFA in relation to my latest politically-motivated ban," he said, in a statement carried on the BBC website.
"I will announce further steps very shortly to challenge this clear abuse of power and process at the hand of FIFA."
Bin Hammam always claimed the FIFA action against him was retribution for having challenged president Sepp Blatter for the presidency.
He was found guilty by FIFA's ethics committee last year of paying bribes to Caribbean Football Union officials at a meeting in Trinidad while campaigning against Blatter for the FIFA presidency.
Jack Warner, who quit as FIFA vice-president after the scandal broke, told officials gifts of 40,000 US dollars each and totalling around one million US dollars had come from Bin Hammam.
Bin Hammam was subject to a 30-day temporary suspension by the AFC, which was extended worldwide by FIFA on July 26.
The suspension by the AFC followed an audit by Pricewaterhouse Coopers (PWC) that centred on contract negotiations and payments to and from AFC bank accounts during Bin Hammam's presidency.
He was alleged to have breached a number of AFC regulations including relating to gifts and bribery.
The PWC report, a copy of which has been seen by the Press Association, raises concerns over broadcast deals signed by Bin Hammam on behalf of the AFC with Al Jazeera and World Sports Groups.
It also states that in 2008 "significant payments (totalling 250,000 US dollars) have also been made to Mr Jack Warner for which no reason has been provided".
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