The Qatari was banned from all football activity for life 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, the 63-year-old's ban was annulled by the Court of Arbitration for Sport on July 19 this year after his appeal was upheld on grounds of insufficient evidence.
He was provisionally suspended by FIFA's ethics committee following the CAS ruling and a statement from FIFA read: "The chairman of the investigatory chamber of the FIFA ethics committee, Michael J Garcia, today [Friday] 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."
Bin Hammam always claimed the FIFA action against him was retribution for having challenged president Sepp Blatter for the presidency, and hailed the decision to annul his lifetime ban last month.
He told BBC World Service: "I promise you I will not quit until I clear my name.
"I have one aim, one mission. one target and that is to clear my name and then I say goodbye.''
Bin Hammam was found guilty by FIFA's ethics committee last year of paying bribes to Caribbean Football Union officials at a meeting in Trinidad last year 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 Asian Football Confederation - the body of which he was president - 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".
Sources close to Bin Hammam said last month that the allegations were a further attempt to tarnish his name.
The CAS panel made its decision by a 2:1 majority and said in its ruling there was no direct evidence to link Bin Hammam with the money's physical presence in Trinidad.
It also questioned why no attempt had been made to trace the banknotes that were photographed. FIFA had hired former FBI director Louis Freeh's firm to investigate the Trinidad payments.
The CAS panel added that "it is more likely than not that Mr Bin Hammam was the source of the monies" and that "his conduct, in collaboration with and most likely induced by Mr Warner, may not have complied with the highest ethical standards that should govern the world of football and other sports".
CAS stressed it was not finding Bin Hammam innocent but that the case was "not proven".
FIFA expressed their concern at the CAS ruling and their ethics committee have now opened fresh proceedings against Bin Hammam.
Bin Hammam had been a growing force in international football and displayed his power by being influential in Qatar's runaway victory in the contest to host the 2022 World Cup.
Some observers had believed he was on course to defeat Blatter in the 2011 presidential race until, less than a month before the election, he was accused of paying around one million US dollars to officials from 25 Caribbean nations.
Witnesses testified that after being addressed by Bin Hammam at a specially-arranged meeting in Trinidad, officials were invited to pick up cash gifts of 40,000 US dollars per association contained in brown envelopes.
The witnesses stated that former FIFA vice-president Warner had told officials afterwards the money had come from Bin Hammam. Warner resigned from FIFA a month later and refused to speak to investigators.
Blatter went on to be elected unopposed after Bin Hammam pulled out of the presidential race, though Football Association chairman David Bernstein unsuccessfully asked the FIFA Congress to postpone the election to allow a new challenger to come forward.