Swiss Domenico Scala stepped down as chairman of FIFA's independent audit and compliance committee, complaining that the reforms were being undermined.
Scala was angered by a decision of the FIFA Congress in Mexico City Friday that will leave the new-look FIFA Council with the ability to appoint and sack members of its committees, including audit, ethics and finance.
Committees had been "deprived of their independence" said Scala in a statement handed to news organizations.
He said he was "consternated about this decision, because it undermines a central pillar of the good governance of FIFA and it destroys a substantial achievement of the reforms."
The new council replaces the old FIFA Executive Committee (ExCo) many of whose former members have been mired in corruption scandals.
"It will henceforth be possible for the council to impede investigations against single members at any time, by dismissing the responsible committee members or by keeping them acquiescent through the threat of a dismissal," Scala added.
FIFA reacted swiftly, claiming Scala had "misinterpreted" the purpose of the decision taken by the FIFA Congress, but accepting his resignation with immediate effect.
He will be replaced on a temporary basis by current deputy chairman Sindi Mabaso Koyana.
"The council fully respects the independence of the Audit and Compliance and the Ethics committees, and any suggestions to the contrary are without merit," said a statement on the FIFA official website.
"Mr. Scala has made unfounded claims which are baseless. FIFA is focused on reform and the path forward as evidenced by the appointment of a new FIFA Secretary-General."
Only three months into his new job, Infantino, who replaced Sepp Blatter at the FIFA helm, has pushed through a number of measures, with the appointment Friday of the new Secretary-General, Fatma Samoura from Senegal.
Samoura, who takes over from Frenchman Jerome Valcke, sacked for his alleged role in the sale of black market World Cup tickets, is the first woman and first non-European to become FIFA's number two.
Italy's Infantino has promised a new era of transparency in the wake of the departure of Blatter, who was handed a six-year ban from football for a breach of ethics.
Scala had been given a key role in helping to drive through changes, but there is clearly a major disagreement over the role of the new council, leading to his shock exit.
"The decision was made to permit the council to appoint members on an interim basis," FIFA claimed in its statement..
"In addition, the measure allows for the swift removal of members who have breached their obligations."
FIFA is still the subject of a criminal investigation in Switzerland, while former senior officials are facing trial in the United States over accusations of kickbacks for television deals.